Electronic Supplementary Material (ESI) for Molecular BioSystems. This journal is © The Royal Society of Chemistry 2015
Supplementary Table 1. 109 D/E-rich repeats containing proteins in yeast
UniProt D/E-rich repeats Protein function Residue pI Start number Length
Histone, nucleosome and kinetochore proteins
O74515 VQPDADEEEEEEEADEMEEEFDEEGEGDEEEEEEDDGDGDGEGDGDGE ASF1_SCHPO Histone chaperone cia1 262 3.57 170 48
Q759F6 EAEDEYPPEQPGVDDEEVDDEDEDEDEDEEGADEEGADEEGASDG ASF1_ASHGO Histone chaperone ASF1 276 3.62 155 45 RKVQTEDEEDDEAEEIDLEAEEEEDEDEEDEDGDEAEEVDEEEEDDDGEPVGA 206 55 SE
Q59MV1 DNEEGADEYPPEQPEDEEEEEEEEEEGEEEEEDEDEEDDDDDEDLNGDAVVDL ASF1_CANAL Histone chaperone ASF1 247 3.62 154 58 EKEEI
P32447 EGDLYPPEQPGVDDEEEEDDEEEDDDEDDEDDEDDDQEDGEGEAEEAAEEEEE ASF1_YEAST Histone chaperone ASF1 279 3.73 158 62 EEEKTEDNE
Q59RN6 TENNEEGDDDDEDEDDDYEQGKLEDEEEEEDELLEIDES CHZ1_CANAL Histone H2A.Z-specific chaperone CHZ1 167 4.02 73 39
Q5AQ47 SSSSSSDNDQDNDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESEINGN HST1_CANAL NAD-dependent protein deacetylase HST1 657 4.23 68 57 QISL
Q8WZM0 IEDEDFQENGIDDEDEEEEEEEAKDEGDEDDEEKGEDDEEDDEEKEGEDGEGE GCN5_YARLI Histone acetyltransferase GCN5 464 4.67 30 71 EEDEEEDEEKKREEEEKY
P34218 KEDEDEDEDFTLDDDIEDEQISEENDEEEDTYEEDSDDDEDG SAS3_YEAST Histone acetyltransferase SAS3 831 6.13 755 42
P53165 DDDNSNDNNNDDDDDDDNDDNEDDDDADDDDD SGF73_YEAST SAGA-associated factor 73 657 9.13 131 32
P32657 MTTIEDDEDEFEDEEGEEDSGEDEDEEDFEEDDDYYGS CHD1_YEAST Chromo domain-containing protein 1 1468 6.15 53 38
P40340 AHDPEEDDESFHEEDVDDDEEEEEADEFEDEYLDEDS TBP7_YEAST Tat-binding homolog 7 1379 4.93 116 37
P25293 AALEFEFEEDEEEADEDEDEEEDDDHGLEDDDGESAEEQDDF NAP1_YEAST Nucleosome assembly protein 417 4.09 363 42
Q9HGN2 TEAMTEEASDEDESVDLEEDEEEEDEEDEEGDEEKQEPPS YO48_SCHPO Putative nucleosome assembly protein 244 4.16 198 40 C36B7.08c
Q12386 SVDPRDVADEEDEDEEGEDEDEDEDDNDVDNEDENDNDNANE ARP8_YEAST Actin-like protein ARP8 881 4.54 70 42 P54784 DVSEDMDSGEISADELEEEEDEEEDEDEEEKEA ORC1_YEAST Origin recognition complex subunit 1 914 5.42 267 33
Q6CA87 VEEVEEEEPEEEEGPEEEEAPEEEVEGDDEEEVQ SWR1_YARLI Helicase SWR1 1772 4.68 123 34 LKEEMTAVEEEEEEELVEEEEEEEEEEEQEEDEEQEQQEEEEEEQEEEVTSR 275 52 LDNIKVERAEEEDEEDEENGDDEDEDEEEDDAEIEEETETTTP 718 43 AIEEDEEEDDAFVIKEEEEEVEVEDDEEEEKAD 816 33
P31380 QSEHEDDDYEEEDEDYNDEEEDVEYDDGDDDDDDDDEFVAT FUN30_YEAST ATP-dependent helicase FUN30 1131 5.12 497 41
P53115 SDIINEKDADEDEEDDEDELEDGEEDMEEDEASTG INO80_YEAST Putative DNA helicase INO80 1489 5.47 132 35 DNENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDF 240 50
Q74Z27 RELSGAKLEDEGEGEDDDEEEDEDDEDDEDEDEDEDEEEEEEEELEELEDIQL INO80_ASHGO Putative DNA helicase INO80 1414 6.36 178 62 LDDDNDKDF
Q6C931 LDLESDDEDQEEEESEFEVSDDEPEDEDEDSEEFA SPT16_YARLI FACT complex subunit SPT16 1003 5.07 931 35
Transcription factors
P38915 ENDSKQDLEGNDDGGEDEEDDDDDDEDDDDDEDEREDDDEQEDDDGEDDAARM SPT8_YEAST Transcription factor SPT8 602 4.13 28 56 DKT
Q6C9G2 ALYDDEDEDGDGADGFIDEDDEDDEEDDEEGEGNGFIDDEVEVDEEDQDEDGD BFR2_YARLI Protein BFR2 495 4.18 78 75 EDMEDEQDEDESDEELSENEND
Q5ACL9 EELDAESAEEEEDEESEDVADDDEDDQESD BFR2_CANAL Protein BFR2 482 4.24 366 43
Q06631 ENEDEEEEEEEEEEKEEDALSFRTDSEDEEVE BFR2_YEAST Protein BFR2 590 4.34 507 51
P36100 KKQAKLNKEEEEEEEEEEDEEEEEEEEMEDVMDDNDETARENA T2EA_YEAST Transcription initiation factor IIE subunit alpha 990 4.81 91 45
Q05021 RSDAETANNVEEEEEEEEEEEEEDEVDEDEEDDEENDEDEDNVHEREHIQE TAF7_YEAST Transcription initiation factor TFIID subunit 7 956 4.88 58 45
O13936 NDKKEDEDNVEENEEEADANEEEEEDEEDDEEDEEDEDESGGGRR SPT5_SCHPO Transcription elongation factor spt5 1063 4.95 134 44
Q5ALX3 EENNEKEQDQEAGQDEEEQDEDEEEEEDDEEEDEEDEVSSRRKRR SPT5_CANAL Transcription elongation factor SPT5 980 5.02 29 47
P27692 KNSDGDTKDEGDNKDEDDDEDDDDDDDDEDDDDEAPTKRRRQER SPT5_YEAST Transcription elongation factor SPT5 720 5.19 606 45 Q6CC84 IKSEEVDKTQDNVEDEDDEEEEEEEEEEEEEDDDEEDVRQRKKPRRE SPT5_YARLI Transcription elongation factor SPT5 683 6.31 526 36
Q59P39 PNTAENDVPGDDEEEEDDDDDDDDDEEEGEQDDEEEEDGSSTSMS EFH1_CANAL Transcriptional regulator EFH1 719 8.00 541 30
P32432 SQNMVEDQDIDDIDDDDDVDDDDDDDDDDDTENGSS SFP1_YEAST Transcription factor SFP1 512 4.46 106 30
Q03213 EDDDDDGDDEGDGRDNEEDSTAEEDEVDDE HOT1_YEAST High-osmolarity-induced transcription protein 1 534 4.53 96 32
P32351 DVDSEEEGEGNDEDDDDGDGDDMDEEESDEEQ IMPX_YEAST Sugar utilization regulatory protein IMP2 346 4.81 95 32
P08638 DEEEEEDEDEEGEEEEEEEELSSKVPENMD LEUR_YEAST Regulatory protein LEU3 886 5.75 678 30
P38114 SNNNDNDNNINDDDDDDDDDDDDDDDDDDDDDNDDDYSNNGADDDEEDDDYDR TBS1_YEAST Uncharacterized transcriptional regulatory 1094 5.12 981 53 protein TBS1
RNA polymerase subunits
P38439 NEYEEDDFLVDDDEEEEAAFDDEEDDNEEEEEEEDADEENASR LEO1_YEAST RNA polymerase-associated protein LEO1 464 4.17 382 43
P36070 QNELDELDDDVDDDDLEEVDLEDDDDLDDDSGDDDDENC RRN3_YEAST RNA polymerase I-specific transcription 627 4.44 245 39 initiation factor RRN3
Q5ALX5 SDNEGGEDIEDDDNDYEDEGDDDEEEEGEEEEEEESDEDEISDIGKS SSN2_CANAL Mediator of RNA polymerase II transcription 1665 4.53 679 47 subunit 13
Q05543 YEVGDGDDDDDDGDNDDDDDDDDDDKNYDDRSND RT103_YEAST Regulator of Ty1 transposition protein 103 409 4.63 263 34
P33441 DEKEESDHEYDDQEDEENEEEDDMEVDVED MFT1_YEAST THO complex subunit MFT1 392 4.27 292 30
Ribosomal proteins
Q06672 RVVHIEGDDDEDDEDVEDYDDEDEDEEMDEVVPDLVS TSR2_YEAST Pre-rRNA-processing protein TSR2 205 3.97 146 37
P39520 DYQAVTDGEESENEEEESEEEEEDDDEDDDDDDDDGSDSDSDSETSSDDEN IFH1_YEAST Protein IFH1 1085 4.37 114 51
Q12136 LLEDEDEEEVLAMDEDDESIDEREDEEEEEEEELDG SAS10_YEAST Something about silencing protein 10 610 4.45 54 36
Q59VP7 SDDEDEEEEQEQEEQPQEEENNSDDDDDDDDDDDDN ERB1_CANAL Ribosome biogenesis protein ERB1 849 4.46 51 36 SSQKEEDNKESDNEDEDEEEDNDDDDDDDEPETSS 571 35 RNA processing
Q751K8 RARGADDGDVDMLDDDDEEEDDDEDEDDEDSDSDVEIIIG FIP1_ASHGO Pre-mRNA polyadenylation factor FIP1 323 4.06 60 40
P38996 TEEEEEEEHQQKGGNDDDDDDNEEEEEEEEDDDDDDDDDDDDEEEEEEEEEEG NAB3_YEAST Nuclear polyadenylated RNA-binding protein 3 802 4.25 86 63 NDNSSVGSDS
Q6C233 DGNGQLVDDYDDDEDDDDEDDEIDEEVDDDLIADENAVDV SQS1_YARLI Protein SQS1 812 4.31 207 40
Q5AFT3 LCFLPFEVIEDDEDEEEEEEEDEEDEDEGEENIDDTKEKKDKK CFT1_CANAL Protein CFT1 1420 4.94 149 43 KIEEKEDNKDDDDNDDDDEDDLYKEEEEEETQ 454 32
P38798 PGKHQAKQDESEDEDDEDDDEDDDDDDDDDDDDGEEGDEDDDEDDDDEDDDDE NMD2_YEAST Nonsense-mediated mRNA decay protein 2 1089 4.85 876 73 EEEDSDSDLEYGGDLDADRD
Q9P6R9 GEEDDDENEEDEEDSEETSESEEDESVNDEK CWC22_SCHPO Pre-mRNA-splicing factor cwf22 887 8.66 368 31
Q6C8C5 KEILGDSDDEEEDDSEAEEEADDEEEEEGDEEEEAQAST CWC22_YARLI Pre-mRNA-splicing factor CWC22 954 8.94 464 39
P11745 SKFDDLEVDDFEEVDSEDEEGEDEEDEDEDEKLEEIETERLEKE RNA1_YEAST Ran GTPase-activating protein 1 407 4.39 345 44
P53107 GYEAIEEDEEEDEEEDEEEGKDGEERKEEEEEENKLEDKD YRB30_YEAST Ran-specific GTPase-activating protein 30 440 4.55 337 40
Q6CFG6 APKKAKVEEEESDDDEEDEEDDDDDDDSDDDDSDDSGEPQMEIK EFG1P_YARLI rRNA-processing protein EFG1 305 4.44 218 44
O74363 FADLSVLEEDDDDEDEDEELEGEKEEEEEEKEKPEISN YND2_SCHPO G-patch and R3H domain-containing protein 695 4.65 257 38 C30B4.02c
Q6CEW9 KGDDEIDEDEDEEEESENKKDDDNEEAEEDEEDPVIED MRD1_YARLI Multiple RNA-binding domain-containing 828 4.98 192 38 protein 1
Q6CAC9 EQELEEDDIEGAGEEEEEVDEEQEEEEDADDAEEDAEDDSETDKYD UTP25_YARLI U3 small nucleolar RNA-associated protein 25 641 5.14 46 46
C4R2K0 KLEEEQEREEEELQEEDEDEDEEDEEINLEDFESDDESHDD UTP25_PICPG U3 small nucleolar RNA-associated protein 25 697 5.56 102 41
Q6CFT1 DFFELAGKTDDGDDEEEDEEDEEEEEEEKE ESF2_YARLI Pre-rRNA-processing protein ESF2 324 5.33 65 30
Q6C2F4 DFENSEEEGEDDEDEAEDDDDEDVEIHEVDEDEDESGDKS NOP14_YARLI Probable nucleolar complex protein 14 832 5.42 360 40
Q6C2Q7 VDPVRDQQEDKMEVEDEEEDEEEDEEDEEEDEEDEEDEEEKEEDDDDDDDEEE NOP12_YARLI Nucleolar protein 12 509 5.47 30 63 IEEPVIKKSK Q59X38 EKEDGEAVEDTDEEEEEVEIEDGDEDQEDEEEEEDEDLKAQKE PESC_CANAL Pescadillo homolog 587 6.13 458 43
Q6C1W9 EGAEGNDEEDDEDDDDEEEEEEESVSAEPEVVE TRM10_YARLI tRNA (guanine(9)-N1)-methyltransferase 371 5.00 318 33
RNA helicase
Q59MW2 DEEEEEEETDESEHESSQDEDINEEEPEEEDED DBP6_CANAL ATP-dependent RNA helicase DBP6 606 4.81 39 33
P32892 MNNGDENQSEEEEEEEEKEEEEEEEEEQEEMTLEKGGKDDE DRS1_YEAST ATP-dependent RNA helicase DRS1 752 5.47 161 41
Q59ZH9 DVEDNETPEVEDEKPTEQEEEEEEEEEEEEEEEEEEEEEEFAGFEDDENNQED MAK5_CANAL ATP-dependent RNA helicase MAK5 782 5.75 97 55 AN
Translation
Q12532 KVKTSGNEDNGDDDEEEEEEEEEEEEEEEEEEEEEEEEKEEEEKEEEQQQDED TAE2_YEAST Translation-associated element 2 1038 5.47 706 59 DSNEVN
Protein-protein interaction
Q59S52 KDSGYNSQNLDDEDEDDEDDDEDDEDEEEEDEDDYDDHDLGTINEGI MDM12_CANAL Mitochondrial distribution and morphology 428 3.90 97 47 protein 12
Q12500 EEVGNSEDNEDDDTDEDSEDDDDDGGDDDDSEDDDDDDDGEGDENGDDGEGDE AVL9_YEAST Late secretory pathway protein AVL9 764 4.20 596 57 NGDD
P38835 TTKDAEDHGEDDGDGDDGEDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDD YHT1_YEAST PH domain-containing protein YHR131C 850 5.02 793 57 GQIT
P40021 NDESSENGDGDNDHDDDYDDDDDDDDDDDESE ZRG8_YEAST Zinc-regulated protein 8 1076 4.60 420 32
Q08979 DEDEFEYEDDEEDEDDGEEEQDAGPLEGDEDEESESDDD KEL3_YEAST Kelch repeat-containing protein 3 651 4.88 518 39
Q99299 IFDGVTVRADEEEEEDEDDEDDEEEEEENDDEEDEEDEEDDEDDEEEEEKRKE AIM44_YEAST Altered inheritance of mitochondria protein 44 758 6.31 642 60 GEGRNLA
P48362 EEMPSKNAEEEEEEESEEEEDDDEEDEIVE HGH1_YEAST FAM203 family protein HGH1 394 4.48 363 30
Ubiquitin related proteins
Q10435 GSESYERDEDVDEEEEEDDDENNDEGDDEDENENDELRSEN YDE1_SCHPO Probable ubiquitin fusion degradation protein 1647 4.82 240 41 C12B10.01c
O74201 VRETVENSWNDDDDEEEEEEDEDEAEDEDDDDDDNIDE UBC2_CANAL Ubiquitin-conjugating enzyme E2 2 179 3.92 141 38
P06104 VKETVEKSWEDDMDDMDDDDDDDDDDDDDEA UBC2_YEAST Ubiquitin-conjugating enzyme E2 2 172 4.02 141 31
Q12161 VDAVDDEDDEEEDEEEEEEMDSDLKDFIEDDEDDEDEDGSR PSH1_YEAST RING finger protein PSH1 406 4.11 254 41
Vesicle
P53076 NSNTSLENDRNDDDDDDDDDDDDDDDDDDDDDESDLESLEGEVDTDTDDN VID30_YEAST Vacuolar import and degradation protein 30 958 4.33 154 50
P38959 ITGSATDAETGDDDDDDDDDDDEDEDDEDEPPLLKY VPS41_YEAST Vacuolar protein sorting-associated protein 41 992 4.63 68 36
P11075 PEETEDTNDKRHDDEGEDGDEDEDEDEDEDEDNGDEDDEDVDSSSSETS SEC7_YEAST Protein transport protein SEC7 2009 4.54 77 49
P53953 YVPLDDDYEVSDEDDEESDGEEEDEDEEEEDVDNSETI SFB2_YEAST SED5-binding protein 2 876 5.05 291 38
P34250 NDKDDDDDKDNDNDDDDDKDDDVNDDDKDENVDDDENVDDDDDDDDDDDDEYH SEG2_YEAS TEisosome protein SEG2 1132 5.47 593 58 DSYDV
Protease/peptidase
P09620 KDKDGDDDNDNDDDDEDDHNSEGDDDDDDDDDEDDNNEKQS KEX1_YEAST Pheromone-processing carboxypeptidase KEX1 729 4.24 544 41
P42781 QKEGDKEDNKGDDKEDGEEDDDDDEDEDDDDASP XPR6_YARLI Dibasic-processing endoprotease 976 4.46 200 34
Protein kinase/phosphatase
Q8TG40 DEGDDNSDSDEYELEEDEQEEEEEREEYDEETNEEME KAD6_CANAL Adenylate kinase isoenzyme 6 homolog HBR1 248 3.92 205 37
Q5AG71 DKIKQHYDDNGDSEEDDEDEDEEEEDDDDDDDARSSFEARP HSL1_CANAL Serine/threonine-protein kinase HSL1 1462 9.34 1122 41
Q75D77 GDDEDDDQDYVDEDSATSEDEEEDVEEEEEEEG PP4R2_ASHGO Serine/threonine-protein phosphatase 4 356 4.03 206 33 regulatory subunit 2
P38193 DDDYREDGADEDDEDDDHMGSTDDDEDDDED PP4R2_YEAST Serine/threonine-protein phosphatase 4 441 4.11 272 31 regulatory subunit 2
Coenzyme A biosynthesis Q08438 DEEDDNKKNDTGGKDEDNDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD VHS3_YEAST Phosphopantothenoylcysteine decarboxylase 674 4.33 588 85 DDDDDDDDDDEDDEDEDEDDEGKKKEDKGGLQ subunit VHS3
P36024 GYPKNNEEEDDDEDEEEDDDEEEDTEDKNENNNDDDDDDDDDDDDDDDDDDDD SIS2_YEAST Phosphopantothenoylcysteine decarboxylase 562 4.41 490 72 DDDDEDEDEAETPGIIDKH subunit SIS2
P36076 DEETGDKEQEQEEQEGADNEDDDDEDDEEDEEDEEEEEALNETASDESNDEED CAB3_YEAST Coenzyme A biosynthesis protein 3 571 4.77 508 60 EEDEEDV
Isomerase
Q6C4C9 LKPADNFDDEDDEDDEDEDDDDEDDEVSAEDMAQIKK FKBP3_YARLI FK506-binding protein 3 407 3.83 59 37 ANEDGLDEVEGGDDDEDDDEDDEMEFEEDDEDDDDEGEIEDFVVCT 100 46
Q59VR3 SNSLLSDDYFEDDDDDEEEDDEEDELDDEEEEEEAEEEKSSKKSN FKBP3_CANAL FK506-binding protein 3 426 4.18 58 45
P38911 DDMDDLDDEEEEEVRIEEVQEEDEEDNDGEEEQEEEEEEEQKEEVK FKBP3_YEAST FK506-binding nuclear protein 411 4.21 201 46
Q06205 SDSDEDEEDYYSDEESSNGEEEEEEEEEDDEELSSGDDDLDD FKBP4_YEAST FK506-binding protein 4 392 4.44 172 42
Transferase
Q5A950 TPAYDTDSDDYDDDEDDDESDKDDEEEEEEENSYDGYDG ATG26_CANAL Sterol 3-beta-glucosyltransferase 1513 5.54 1462 39
P32784 IGENTAREEEEEEEEEEEEEEEEEEGKEGD GPT1_YEAST Glycerol-3-phosphate O-acyltransferase 1 759 6.97 729 30
Phospholipase
Q5AM72 NEDKKLLDELDNEDEEEDEEEEEVDVDDDDDDDDDSLSDSFEIT PLPL_CANAL Patatin-like phospholipase domain-containing 853 4.95 798 44 protein CaO19.1504
Stress
Q5A2K0 FEELDDEHDQENEDEELEDDEEDYYDEYDDDEEEDEEEDEDDDDIEEEGASDT NST1_CANAL Stress response protein NST1 1399 5.61 620 62 ESEISEEEK
Electron transfer
P00127 EQHEEKAAEGEEKEEENGDEDEDEDEDEDDDDDDDEDEEEEEEVTDQLEDLRE QCR6_YEAST Cytochrome b-c1 complex subunit 6 147 3.83 31 56 HFK Transporter
Q9UUA5 EDEIMDEEFGYDDDDDEEFDLDDLDDLEEE MTXL_SCHPO Metaxin-like protein C409.19c 450 4.48 419 30
O59712 SEAQPEVQGNDDEVEEEDDDDDDEDEDEDEDEDNNNNNRWL YBH4_SCHPO Uncharacterized transporter C3B8.04c 867 5.94 190 41
Unknown proteins
P53288 LSEDDEEEDSESEDEDEDEDSDSDSDSDSDSDEDEDEDEDSEEEEETA YG3R_YEAST Putative uncharacterized protein YGR160W 203 2.94 122 48
Q9P6R2 DLEENEEDDLGDFIAEEEEEEEQEEEQEEDEEDEEEVG YOH8_SCHPO Uncharacterized protein C13E7.08c 429 4.27 326 38
P43611 PIFETDSETEDYEDDENENEDEDEDEDEDDVGIEDENKEYEFD YFK9_YEAST Uncharacterized protein YFR039C 510 4.53 165 43
Q04007 GFNYDDEEGGNEDNYDDDEDDDDDDDDDDESDDEGLS YDR86_YEAST Uncharacterized protein YDR186C 877 5.05 467 37
P53907 EDVNGDEDDDEDEDDANYEEDDEDGYVEDDD YNO4_YEAST Uncharacterized protein YNL144C 740 6.17 551 31
Supplementary Table 2. Interacting proteins of five D/E-rich repeats containing proteins with unknown functions in yeast
(A). P53288 (YG3R_YEAST Putative uncharacterized protein YGR160W)
203aa pI=2.94 D+E=28+36=64 (32%)
Database Interacting protein(s) BioGRID No data
DIP Telomere elongation protein EST1*
IntAct Telomere elongation protein EST1* Something about silencing protein 10* ADP-ribosylation factor-like protein 3*
STRING Nuclear localization sequence-binding protein (p67)* Telomere elongation protein EST1* Ribosome biogenesis protein BRX1* NET1-associated nuclear protein 1* Ribosome biogenesis protein NSA2* Something about silencing protein 10* Ribosome biogenesis protein YTM1* Pescadillo homolog poly(A) RNA binding* tRNA guanosine-2'-O-methyltransferase TRM11* ATP-dependent RNA helicase DBP2*
*: DNA/RNA related proteins
(B). Q9P6R2 (YOH8_SCHPO Uncharacterized protein C13E7.08c)
429aa pI=4.27 D+E=37+63=100 (23%)
Database Interacting protein(s) BioGRID Histone H2A variant Pht1* RNA-binding protein* DASH complex subunit Ask1* Protein phosphatase type 2A, intrinsic regulator (predicted) RNA lariat debranching enzyme Dbr1* Elongator complex, histone acetyltransferase subunit Elp3 (predicted)* Elongator complex subunit Elp2 (predicted)* Argonaute* SWI/SNF and RSC complex subunit Arp42* MBF transcription factor complex subunit Res2* DASH complex subunit Dad2* Retromer complex subunit Vps17RNA polymerase II associated Paf1 complex subunit Tpr1* RNA polymerase II associated Paf1 complex (predicted)* Mitotic spindle checkpoint protein Dma1 Tor Complex Tor2 interacting protein 1 AP-3 adaptor complex subunit Apl5 (predicted) SNARE Fsv1 Glutamate 5-kinase (predicted) Cyclin Clg1 (predicted) G-protein coupled receptor Git3 AP-3 adaptor complex subunit Apm3 (predicted) WD repeat protein Swd3 Palmitoyltransferase (predicted) Alpha-1,2-galactosyltransferase (predicted) Imidazoleglycerol-phosphate synthase Xap-5-like protein Mediator complex subunit Med19/Rox3* Transcription elongation factor TFIIS* Mediator complex subunit Pmc1* Splicing factor Cwf28* Histone promoter control protein Hpc2 (predicted)* DASH complex subunit Spc19* Anaphase-promoting complex subunit Apc10 Autophagy associated protein Atg13 (predicted) DASH complex subunit Dad3* Splicing factor Sap114* SAGA complex subunit Sgf29 (predicted)* TFIIH complex cyclin Mcs2* DASH complex subunit Dam1* DASH complex subunit Dad4* AAA family ATPase Gcn20 (predicted) Vacuolar SNARE Vam7 (predicted) Linear element associated protein Hop1 MAP kinase Sty1 F-box protein Pof9 Golgi membrane exchange factor subunit Sat1 (predicted) Ubiquitin C-terminal hydrolase Ubp3 Uridine kinase/uracil phosphoribosyltransferase (predicted) IPT/TIG ankyrin repeat protein SAGA complex histone acetyltransferase subunit Gcn5* Ash2-trithorax family protein Mediator of replication checkpoint 1 DNA repair nuclease Rad13* DNA repair endonuclease Swi10* WD repeat protein Vps8 Autophagy associated protein Aut12 (predicted) GTPase Ryh1 Tyrosine phosphatase Pyp1 P-TEFb-associated cyclin-dependent protein kinase Lsk1 Alpha-1,2-galactosyltransferase (predicted) Lid2 complex subunit Snt2 Retromer complex subunit Vps35 Pho85/PhoA-like cyclin-dependent kinase Pef1 RNA-silencing factor Ers1* Adenosine deaminase Ada1 (predicted) Cell wall protein Asl1, O-glucosyl hydrolase (predicted) ATP-dependent DNA helicase Hrp3* Sister chromatid cohesion protein/DNA polymerase eta Eso1* Hypothetical protein RNA-directed RNA polymerase Rdp1* Phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Helicase Required for RNAi-mediated heterochromatin assembly Hrr1* CCR4-Not complex subunit Ccr4 (predicted)* Dicer* AP-3 adaptor complex subunit Apl6 (predicted)
DIP No data
IntAct No data
STRING Cell division control protein 73 FACT complex subunit spt16* Tetratricopeptide repeat protein 1 RNA polymerase II-associated protein 1 homolog* FACT complex subunit pob3* Transcription elongation factor spt5* RNA polymerase-associated protein C651.09c* Cyclin pch1 Transcription elongation factor spt4* CTD kinase subunit alpha
*: DNA/RNA related proteins
(C). P43611 (YFK9_YEAST Uncharacterized protein YFR039C)
510aa pI=4.53 D+E=39+53=92 (18%)
Database Interacting protein(s) BioGRID Polyubiquitin Target of rapamycin complex subunit LST8 Mitogen-activated serine/threonine protein kinase FUS3 U1 small nuclear ribonucleoprotein 70 kDa homolog* Histone deacetylase RPD3* Ribosome biogenesis protein BMS1* Centractin GPI-anchor transamidase Nuclear migration protein JNM1
DIP Target of rapamycin complex subunit LST8 U1 small nuclear ribonucleoprotein 70 kDa homolog*
IntAct No data
STRING Target of rapamycin complex subunit LST8 Putative uncharacterized protein YJR037W GRAM domain-containing protein YSP2 U6 snRNA phosphodiesterase* Uncharacterized protein YDR186C Ubiquitin-conjugating enzyme suppressor 1 Uncharacterized protein YHR080C Protein MNE1 Uncharacterized ATP-dependent helicase YFR038W* Uncharacterized transporter YJL193W
*: DNA/RNA related proteins
(D). Q04007 (YDR86_YEAST Uncharacterized protein YDR186C)
877aa pI=5.05 D+E=72+44=116 (13%)
Database Interacting protein(s) BioGRID Protein phosphatase 2C homolog 4 Polyubiquitin Heat shock protein SSB1 Rho-type GTPase-activating protein 1 Single-stranded nucleic acid-binding protein* hnRNP arginine N-methyltransferase* Heterogeneous nuclear rnp K-like protein 2* mRNA-binding protein PUF3* Conserved oligomeric Golgi complex subunit 5 Protein SNO4 Conserved oligomeric Golgi complex subunit 6 Clathrin light chain Ceramide very long chain fatty acid hydroxylase SCS7 Protein GRE1 Probable oxidoreductase ENV9 Casein kinase II subunit beta' U1 small nuclear ribonucleoprotein C* Phosphatidylethanolamine N-methyltransferase Mitochondrial import inner membrane translocase subunit TIM13 Prohibitin-1 Acyl-CoA desaturase 1 Protein RPN4 Nuclear membrane organization protein APQ12 Phosphatidyl-N-methylethanolamine N-methyltransferase Protein OR Protein transport protein SEC22 Protein transport protein BOS1 Inositol phosphorylceramide synthase catalytic subunit AUR1 Histone-specific N-acetyltransferase NAT4*
DIP Protein phosphatase 2C homolog 4
IntAct Heat shock protein SSB1 Heat shock protein SSA2 Protein phosphatase 2C homolog 4 Rho-type GTPase-activating protein 1 tRNA(His) guanylyltransferase* ATP-dependent molecular chaperone HSP82 Ubiquitin-conjugating enzyme E2 2 Heat shock protein SSA1 5'-AMP-activated protein kinase subunit gamma T-complex protein 1 subunit gamma Heat shock protein SSB2 6-phosphofructo-2-kinase 1 T-complex protein 1 subunit theta Auxilin-like clathrin uncoating factor SWA2 Heat shock protein 42 Flavohemoprotein Autophagy-related protein 33
STRING Protein phosphatase 2C homolog 4 Rho-type GTPase-activating protein 1 Sphingoid long-chain base transporter RSB1 Nuclear protein SNF4* Flavohemoprotein U6 snRNA phosphodiesterase* Acyl-CoA desaturase 1 Probable oxidoreductase ENV9 Ubiquitin-conjugating enzyme suppressor 1 Uncharacterized transporter YJL193W
*: DNA/RNA related proteins
(E). P53907 (YNO4_YEAST Uncharacterized protein YNL144C)
740aa pI=6.17 D+E=61+43=104 (14%)
Database Interacting protein(s) BioGRID DNA topoisomerase 2-associated protein PAT1* Polyubiquitin Actin cytoskeleton-regulatory complex protein SLA1 Zinc finger protein GIS2 Nuclear polyadenylated RNA-binding protein NAB2* SCF E3 ubiquitin ligase complex F-box protein GRR1 Genetic interactor of prohibitins 3, mitochondrial Fatty acyl-CoA synthetase and RNA processing-associated kinase 1*
DIP No data
IntAct Actin cytoskeleton-regulatory complex protein SLA1 Protein RCR1 Protein JSN1 Heat shock protein SSB1 Heat shock protein homolog SSE1 Heat shock protein SSB2
STRING Protein MBR3 Respiratory growth induced protein 1 Serine/threonine-protein kinase MRK1 Protein RCR1 Protein MTH1 Serine/threonine-protein phosphatase 1 regulatory subunit GAC1 Uncharacterized protein YMR206W Maltose permease MAL31 Glycogen synthesis initiator protein GLG1 Nuclear polyadenylated RNA-binding protein NAB2*
*: DNA/RNA related proteins
Supplementary Table 3. 173 D/E-rich repeats containing proteins in PDB databank
PDB D/E-rich repeats Protein function Residue pI Start number Length
Histone, nucleosome, and chromatin protein 2JSS_B GN EGEEEEDDLAEID NMR structure of chaperone CHZ1 complexed with histone H2A.Z-H2B 62 3.97 19 15 4CAY_C KEEIQDEEDDDDYV Crystal structure of a human ANP32E-H2A.Z-H2B complex 23 3.13 9 14 4IOY_X EDELEQEQEE Structure of the SPT16 middle domain reveals functional features of the histone chaperone FACT 243 5.19 90 10 2AYU_A NEDQDEELEEDLEER The structure of nucleosome assembly protein suggests a mechanism for histone binding and shuttling 283 4.20 236 15 1GUW_A VEEVLEEEEEEYVVE Structure of the chromodomain from mouse HP1beta in complex with the lysine 9-methyl histone H3 N-terminal 73 4.20 3 15 peptide, NMR, 25 structures 2RSO_A KEEEGGEEEEEDEYVVE Solution structure of the chromodomain of SWI6 92 4.63 18 17 4ACO_A EDLDEEEENS Structure of the budding yeast NDC10 N-terminal domain 452 6.41 49 10 1Q2Y_A EEEIDELENE Crystal structure of the protein YJCF from Bacillus subtilis: a member of the GCN5-related N-acetyltransferase 140 5.56 32 10 superfamily fold 2DEW_X EDDEVLDSED Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8 629 5.61 140 10 1C3P_A DFEEFDDEVD Crystal structure of an HDAC homolog from Aquifex aeolicus 372 5.75 333 10 2XSZ_F CEEEDVESEDA The dodecameric human RUVBL1:RUVBL2 complex with truncated domains II 301 5.56 225 11
Transcription factor 3T5V_F EE DDEFEDFP SAC3:THP1:SEM1 complex 47 3.50 1 10 1MJE_B LLEEDDEFEEFP Structure of a BRCA2-DSS1-ssDNA complex 42 3.59 6 12 4B0A_A DAVDFEDEDELADD The high-resolution structure of YTBP-YTAF1 identifies conserved and competing interaction surfaces in 237 5.56 45 14 transcriptional activation 1NGM_N DNLEDVDDEE Crystal structure of a yeast BRF1-TBP-DNA ternary complex 53 4.16 7 10 2RNQ_A EEDEEEDDEFEEVADD Solution structure of the C-terminal acidic domain of TFIIE alpha 62 3.59 1 16 1HV2_A EDDDEIPEFE Solution structure of yeast elongin c in complex with a von Hippel-Lindau peptide 99 4.16 72 10 2F8X_C LDDDESEGEEF Crystal structure of activated NOTCH, CSL and MAML on HES-1 promoter DNA sequence 424 7.81 201 11
DNA methylation 3SWR_A KEADDDEEVDDNI Structure of human DNMT1 (601-1600) in complex with sinefungin 965 8.23 84 13 3PT6_B KEADDDEEADDDVSE Crystal structure of mouse DNMT1 (650-1602) in complex with DNA 915 8.23 51 15
DNA helicase and recombinase 2JPN_A ELEDSDDEVEES Solution structure of T4 bacteriophage helicase UVSW.1 79 4.16 67 12 3PJR_A SLEDDDEMEEERR Helicase substrate complex 646 5.28 584 13 2P6R_A DWIEEKDEDE Crystal structure of superfamily 2 helicase HEL308 in complex with unwound DNA 683 6.03 566 10 3LHF_D EDKEEELVED The crystal structure of a serine recombinase from Sulfolobus solfataricus to 2.3Å 140 7.63 99 10
ssDNA binding protein 1JE5_B EDDWADEVEE Crystal structure of GP2.5, a single-stranded DNA binding protein encoded by bacteriophage T7 182 4.91 167 10
RNA polymerase subunit 1QKL_A DGDDFDDVEEDEGLDDLE HRPABC14.4, essential subunit of human RNA polymerases I II and III 127 3.92 9 18 2KX2_A DEDTERDDGD The solution structure of MTH1821 96 4.06 43 10 3H0G_M DDDRKAEDDDNMIEED RNA polymerase II from Schizosaccharomyces pombe 1476 5.66 1247 16
Ribosomal protein 2ZKR_5 DDVLDEDELEE Structure of a mammalian ribosomal 60S subunit within an 80S complex obtained by docking homology models of 210 3.97 76 11 the RNA and proteins into an 8.7 Å cryo-EM map 4BEH_B KEESEESDDDM Solution structure of human ribosomal protein P1.P2 heterodimer 116 4.25 100 11 3O5H_E MEELADDDEER Yeast 80S ribosome. this entry consists of the 60S subunit of the second 80S in the asymmetric unit. 287 6.13 200 11 3IZR_Q AGADDDDEEEDD Localization of the large subunit ribosomal proteins into a 5.5 Å cryo-EM map of Triticum aestivum translating 80S 304 9.31 292 12 ribosome 3IZ6_A EEAKEQEEEE Localization of the small subunit ribosomal proteins into a 5.5 Å cryo-EM map of Triticum aestivum translating 80S 260 5.19 212 10 ribosome 3J13_H EAGDSEEEEE Structural characterization of mrna-trna translocation intermediates (30S ribosome of class 3 of the six classes) 135 4.81 125 10 3GU0_A DEELEKEAEE Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone 406 4.65 353 10
Translation factor 1D7Q_A FDDIGDDDEDIDD Human translation initiation factor EIF1A 143 4.91 130 13 4N3S_B PEDDEDELMDDV Crystal structure of eukaryotic translation initiation factorEIF5B (399-852) from Saccharomyces cerevisiae, apo 442 5.19 316 12 form 4N3N_A GPDDDEEELEEEVESD Crystal structure of eukaryotic translation initiation factor EIF5B (517-1116) from Chaetomium thermophilum, apo 587 6.69 314 16 form 2IU1_A SGGEEEDEDENIEV Crystal structure of EIF5 C-terminal domain 178 5.19 159 14 2IW3_B NFDDEEDEGEDLC Elongation factor 3 in complex with ADP 958 5.56 415 13 1ZQ1_D DDERDELFEE Structure of GATDE tRNA-dependent amidotransferase from Pyrococcus abyssi 508 6.13 478 10
RNA cleavage 4OO1_F DDGDDEDLLE Structure of an RRP6-RNA exosome complex bound to poly(A) RNA 207 4.81 175 10 1WMI_D EERDEDITEEE Crystal structure of archaeal RELE-RELB complex from Pyrococcus horikoshii OT3 61 3.69 24 11 2GTI_A EEKDFDLDDD Mutation of MHV coronavirus non-structural protein NSP15 (F307L) 343 5.56 214 10 4OAU_C GEDVENEEDEF Complete human RNase l in complex with biological activators 692 6.27 426 11
RNA splicing 4A4F_A EAEIEEIDEE Solution structure of SPF30 tudor domain in complex with symmetrically dimethylated arginine 64 3.88 27 10 1ZYI_A VAEEEDSDDDVEP Solution structure of ICLN, a multifunctional protein involved in regulatory mechanisms as different as cell volume 116 4.06 77 13 regulation and RNA splicing 4FXW_C EELLDDEEYEEIVED Structure of phosphorylated SF1 complex with U2AF65-UHM domain 101 4.34 15 15 2Y9D_T GVEEEEEDGEMR Structure of the spliceosomal U4 snRNP core domain 83 4.44 71 12
mRNA triphosphatase 3V85_A RVEEDEEEIEYW 1.9 angstrom resolution crystal structure of the protein Q9SIY3 from Arabidopsis thaliana 204 5.38 81 12
RNA binding 4N0L_B EEEDKDEAADE Methanopyrus kandleri CSM3 crystal structure 334 4.58 277 11 4GUA_C KDEDMEIDDEL Alphavirus p23pro-zbd 662 8.42 502 11 2M4G_A EEELLERDEEE Solution structure of the core domain (11-85) of the murine norovirus VPG protein 75 5.75 42 11
Signal recognition particle 4C7O_D DDDLFEELEE The structural basis of FTSY recruitment and GTPase activation by SRP RNA 277 5.09 5 10 1VMA_B DDETREELEE Crystal structure of cell division protein FTSY (TM0570) from Thermotoga maritima at 1.60 Å resolution 294 5.38 32 10
1ZU4_A DDEFFEELED Crystal structure of ftsy from Mycoplasma mycoides- space group p21212 305 6.50 28 10 3E70_C VEEEVEKEEEEV Structures and conformations in solution of the signal recognition particle receptor from the archaeon Pyrococcus 307 5.38 16 12 furiosus
Ca2+ regulation 1YO8_A DACDDDDDND Structure of the C-terminal domain of human thrombospondin-2 616 4.04 187 10 3H4S_A EEEDLVDIEED Structure of the complex of a mitotic kinesin with its calcium binding regulator 359 8.75 346 11
1OQP_A NDDNEIDEDEF Structure of the Ca2+/C-terminal domain of caltractin in complex with the CDC31P-binding domain from KAR1P 77 4.16 57 11
1SNL_A EEDDMREMEEE NMR solution structure of the calcium-binding domain of nucleobindin (CALNUC) 99 4.30 55 11 4JRF_A DPGEDDDDKE Crystal structure of a putative cell adhesion protein (BACOVA_01548) from Bacteroides ovatus ATCC 8483 at 469 4.34 443 10 1.98 Å resolution (PSI community target, Nakayama) Transporter 2DPK_A IDDDIFEEDEN The crystal structure of the primary Ca2+ sensor of the Na+/Ca2+ exchanger 124 4.11 79 11 3RB5_B IDDDVFEEDEC Crystal Structure of calcium binding domain CBD12 of CALX1.1 245 4.34 73 11 3NAF_A LDQDDDDDPDTEL Structure of the intracellular gating ring from the human high- conductance Ca2+ gated K+ channel (BK channel) 648 5.75 480 13
4EV6_E LEDELEELEDK The complete structure of CORA magnesium transporter from Methanocaldococcus jannaschii 317 5.00 154 11 4I0U_J DDEIDVLEEE Improved structure of Thermotoga maritima CORA at 2.7 Å resolution 345 5.38 185 10 4HG0_A GEIEDEYDEEDDIDF Crystal structure of magnesium and cobalt efflux protein CORC, Northeast structural genomics consortium (NESG) 221 4.39 131 15 target ER40 3DXS_X EEDIKEEIED Crystal structure of a copper binding domain from HMA7, a p-type ATPase 77 4.06 55 10 3HUT_A DDVIDEIEDE Crystal structure of a putative branched-chain amino acid ABC transporter from Rhodospirillum rubrum 341 4.63 179 10 4Q4A_B DLEEEKDDPD Improved model of AMP-PNP bound TM287/288 584 9.13 326 10 1MHS_B PKVEDDEDEDIDAL Model of Neurospora crassa proton ATPase 920 4.91 34 14 DGHDAEEEEEEAT 56 13 Sensor 1YAX_D EVREDDDDAE Crystal structure analysis of S.typhimurium PHOQ sensor domain with calcium 134 4.72 93 10 2ZIY_A DDKETEDDKD Crystal structure of squid rhodopsin 370 6.69 337 10 Protein kinase and phosphatase 3V8S_D DDLEEDKGEEE Human rho-associated protein kinase 1 (ROCK 1) in complex with indazole derivative (compound 18) 397 4.77 364 11 3A7I_A DLEEAEDEIEDI Human MST3 kinase in complex with adenine 286 5.75 44 12 4OBO_B MDVTEDEEEEIKLE MAP4K4 in complex with inhibitor (compound 22), 6-(3-chlorophenyl) quinazolin-4-amine 297 7.63 42 14 2OIB_D DIKEEIEDEE Crystal structure of IRAK4 kinase domain apo form 288 5.09 227 10 3HZH_B FEEYDDFDDEETKE Crystal structure of the CHEX-CHEY-BEF3-Mg2+ complex from Borrelia burgdorferi 149 4.16 67 14 1J9L_B EVIEDDDRDDVDY Crystal structure of SURE protein from T.maritima in complex with vanadate 247 4.81 204 13
Oxygenase and reductase 2WGK_B EELEGEEGDE Type II Baeyer-Villiger monooxygenase oxygenating constituent of 3,6-diketocamphane 1,6 monooxygenase from 368 5.38 162 10 Pseudomonas putida 4HHR_A LKDEDDDLEDEDLY Crystal structure of fatty acid alpha-dioxygenase (Arabidopsis thaliana) 640 5.94 291 14 3WG6_D DFELDKEDED Crystal structure of conjugated polyketone reductase c1 from Candida parapsilosis complexed with NADPH 298 6.31 268 10 3AGC_B DAEEEDKLEE F218V mutant of the substrate-bound red chlorophyll catabolite reductase from Arabidopsis thaliana 260 5.28 176 10 4NTD_A DDVEREGEDD Crystal structure of HLMI 319 5.38 85 10 1SEN_A LEDEEEPKDEDF Endoplasmic reticulum protein RP19 O95881 134 4.81 65 12 2A4H_A VEDADGDDDEDY Solution structure of SEP15 from Drosophila melanogaster 126 6.31 109 12
Hydrolase and dehydrolase 1XM5_D DHIEDDEAEEMEA Crystal structure of metal-dependent hydrolase YBEY from E. coli, PFAM UPF0054 152 4.06 123 13 1QLM_A EEIDYEDDAD The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon 316 3.80 124 10 Methanopyrus kandleri 4BJZ_A DVELDEDIED Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid-assisted flavoprotein strategy for 395 4.91 192 10 regioselective aromatic hydroxylation: native data 1UMD_C EEWEEDVREE Branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methyl-2-oxopentanoate 361 5.38 307 10 as an intermediate 4I14_B DDEDRENEGD Crystal structure of MTB-RIBA2 (RV1415) 320 5.19 24 10
Isomerase 4DOK_B AEEDKYEEEEETELEK Crystal structure of Arabidopsis thaliana chalcone-isomerase like protein AT5G05270 (AtCHIL) 208 4.63 113 16 4MSP_B EDIFDKEDED Crystal structure of human peptidyl-prolyl cis-trans isomerase FKBP22 (akaFKBP14) containing two EF-hand 189 5.56 164 10 motifs Protease and peptidase 4IC5_C EELEEEEERN Crystal structure of DEG5 209 4.53 1 10 1QXP_B EEVDDADDYD Crystal structure of a mu-like calpain 788 5.23 370 10 4HXF_B EDEDFIFEDD Acylaminoacyl peptidase in complex with z-gly-gly-phe-chloromethyl ketone 613 5.56 122 10 3IJ3_A DDFEDDEYYE 1.8 angstrom resolution crystal structure of cytosol aminopeptidase from Coxiella burnetii 457 5.56 93 10
Synthase 3MIO_B DDEDRENEGD Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from Mycobacterium tuberculosis at 194 4.72 24 10 pH 6.00 4QLB_D EDLDEEEVLE Structural basis for the recruitment of glycogen synthase by glycogenin 651 6.13 17 10 1XPM_D DDVEFDEEQD Crystal structure of Staphylococcus aureus HMG-CoA synthase with HMG-CoA and acetoacetyl-CoA and 415 4.72 379 10 acetylated cysteine 2FQ1_B DESDEPFDDD Crystal structure of the two-domain non-ribosomal peptide synthetase ENTB containing isochorismate lyase and 279 4.91 224 10 aryl-carrier protein domains 4DG8_A VTDDDLEEDDIP Structure of PA1221, an NRPS protein containing adenylation and PCP domains 495 6.50 307 12 1TKS_B DDEDRENEGD Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans 196 4.91 23 10 1WEO_A RVEGDEDEEDIDSG Solution structure of ring-finger in the catalytic subunit (IRX3) of Cellulose synthase 93 4.44 76 14 4L4X_A DELLDDEELDD An A2-type ketoreductase from a modular polyketide synthase 503 4.58 379 11
Transferase 3A8T_A SPEDEDHDEDSA Plant adenylate isopentenyltransferase in complex with ATP 289 5.47 162 12 4HNY_B DCEDSDEQDEND Apo N-terminal acetyltransferase complex A 216 4.81 52 12 2HY5_B EDMETEEEFD Crystal structure of DSREFH 132 4.06 99 10
Kinase and phosphorylase 1BO1_A EVEERAEDEE Phosphatidylinositol phosphate kinase type II beta 326 5.66 260 10 3DDS_B DIEELEEIEEDA Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261 802 6.50 96 12 2GJ4_A DMEELEEIEEDA Structure of rabbit muscle glycogen phosphorylase in complex with ligand 803 6.69 107 12
Mutase 3I3W_B DDALEEEVEDIDGD Structure of a phosphoglucosamine mutase from francisella tularensis 433 5.38 117 14
Enolase 3UJ2_H EDGLDEEDWE Crystal structure of an enolase from Anaerostipes caccae (EFI target EFI-502054) with bound Mg2+ and SO42- 423 4.72 285 10
Glucosidase 4J5T_A DEYEEILEDE Crystal structure of processing alpha-glucosidase I 788 4.86 511 10
Cystathionase 3COG_D LEDEEDLLEDLD Crystal structure of human cystathionase (cystathionine gamma lyase) in complex with dl-propargylglycine 392 6.41 371 12
Penicillin binding protein 3TG9_B DEEITDDFED The crystal structure of penicillin binding protein from Bacillus halodurans 326 5.09 103 10 1W5D_A DEEDGKDIED Crystal structure of PBP4A from Bacillus subtilis 458 5.09 440 10
Lactamase 3LEZ_A RDEEDADYDDK Crystal structure of a halotolerant bacterial beta-lactamase 261 3.90 236 11
Lipid transfer 4B2Z_B IDTDDIDEDDESG Structure of osh6 in complex with phosphatidylserine 400 6.69 1 13
Signaling 1GSM_A EEEEEPQGDED A reassessment of the madcam-1 structure and its role in integrin recognition. 206 5.00 148 11 4F7Z_A EEEKKECDEE Conformational dynamics of exchange protein directly activated by cAMP 946 6.36 269 10
Electron transfer 3QG2_B DDEEEDDFVY Plasmodium falciparum DHFR-TS qradruple mutant (N51I+C59R+S108N+I164L, V1/S) pyrimethamine complex 542 7.63 217 10 2WLB_B LDPPEEDEEDMLDL Adrenodoxin-like ferredoxin ETP1FD (516-618) of Schizosaccharomyces pombe mitochondria 101 3.97 60 14 1L5P_C EDDEKEFLED Crystal structure of Trichomonas vaginalis ferredoxin 93 4.44 60 10 3AH7_A LEEADELEEDM Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FDXB) from Pseudomonas putida JCM 20004 109 4.44 62 11 1NXI_A LEAEETEDEDG Solution structure of Vibrio cholerae protein VC0424 132 4.11 68 11
Ubiquitin binding protein 2KLZ_A EIDMEDEEAD Solution structure of the tandem UIM domain of ataxin-3 complexed with ubiquitin 46 3.88 20 10 1WHC_A EHEDDPDVDE Solution structure of RSGI RUH-027, a UBA domain from mouse cDNA 64 3.88 47 10 2DAI_A LDEDEDERVDEA Solution structure of the first UBA domain in the human ubiquitin associated domain containing 1 (UBADC1) 83 4.06 20 12 2XZE_Q SEDEEEEEEALEA Structural basis for AMSH-ESCRT-III CHMP3 interaction 23 3.69 1 13 1Q0V_A QEIEEEEDPDL Solution structure of tandem UIMs of VPS27 81 4.34 48 11 3M62_A DEEEDLEYGD Crystal structure of UFD2 in complex with the ubiquitin-like (UBL) domain of RAD23 955 5.47 871 10 2KIZ_A EEGTEEDTEE Solution structure of arkadia RING-H2 finger domain 69 4.25 6 10 3T6P_A EDEKREEEKE IAP antagonist-induced conformational change in CIAP1 promotes E3 ligase activation via dimerization 330 5.94 152 10
Chaperone 2KGL_A EKDDDIEEGD NMR solution structure of MESD 195 5.75 33 10 1JHN_A EDWDEDMDGE Crystal structure of the lumenal domain of calnexin 380 4.48 263 10 2Z5B_B DDEEEEFVRD Crystal structure of a novel chaperone complex for yeast 20S proteasome assembly 132 4.53 51 10 3VL1_B LEENDENDDEF Crystal structure of yeast RPN14 416 5.00 18 11 2O1T_J VEEEPEEEPE Structure of middle plus C-terminal domains (m+c) of GRP94 413 5.84 403 10 2CG9_B DFELEETDEE Crystal structure of an HSP90-SBA1 closed chaperone complex 618 4.95 481 10
Nuclear import and export 2QNA_A KQDENDDDDDWN Crystal structure of human importin-beta (127-876) in complex with the IBB-domain of snurportin1 (1-65) 744 4.44 207 12 3W3W_A IESDDTDDEEEVT Crystal structure of KAP121P bound to STE12P 1028 4.54 318 13 3IBV_B EWDDDPDSEEEAE Karyopherin cytosolic state 902 4.58 393 13 1WA5_C EEDVELFEDD Crystal structure of the exportin CSE1P complexed with its cargo (KAP60P) and RANGTP 937 5.23 343 10
Protein assembly 3U2G_A DVELDDIEDEDDVV Crystal structure of the C-terminal DUF1608 domain of the Methanosarcina acetivorans s-layer (MA0829) protein 269 3.50 163 14 2JKG_A EDYDIEVEDE Plasmodium falciparum profilin 165 4.11 53 10 3JVO_M IEFEEDDRDEL Crystal structure of bacteriophage HK97 GP6 92 4.25 17 11 1PZD_A EADDEGYEDE Structural identification of a conserved appendage domain in the carboxyl-terminus of the COPI gamma-subunit. 271 4.30 138 10 1R4X_A ETDDEGYEDE Crystal structure analys of the gamma-COPI appendage domain 273 4.58 141 10 3UC9_A EEVEQDEIDE Crystal structure of yeast IRC6P - a novel type of conserved clathrin accessory protein 180 4.53 120 10 2FPF_D EDELELEVDD Crystal structure of the IB1 SH3 dimer at low resolution 60 4.44 16 10 2YCU_A DEGEEEAEVE Crystal structure of human non muscle myosin 2C in pre-power stroke state 962 6.59 24 10 1HQZ_9 RDEDDLDENEL Cofilin homology domain of a yeast actin-binding protein ABP1P 137 4.44 120 11 3J47_V EEEKELTEEE Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid 63 4.63 27 10
Others 3FM0_A WEVDEEDEYEC Crystal structure of WD40 protein CIAO1 328 4.81 128 11 1LXD_B LDEDEPEDYEL Crystal structure of the RAS interacting domain of RALGDS, a guanine nucleotide dissociation stimulator of RAL 87 4.63 42 11 protein 2RGF_A LEEEEPEDYEL RBD of RAL guanosine-nucleotide exchange factor (protein), NMR, 10 structures 97 4.81 51 11 2AFF_B ELNDDDKDDE The solution structure of the Ki67FHA/hNIFK(226-269)3p complex 37 4.25 21 10 2O5N_B EDDILEDDIED Crystal structure of a viral glycoprotein 267 4.67 181 11 2WVI_A EKEEEEEVFE Crystal structure of the N-terminal domain of BUBR1 160 4.81 149 10 2GD5_D IEEEEAEEIDR Structural basis for budding by the ESCRTIII factor CHMP3 149 10.06 125 11 2HR0_B PEEDECQDEEN Structure of complement C3B: insights into complement activation and regulation 907 5.05 876 11 4AQB_A DECKEREDEE MBL-ficolin associated protein-1, map-1 aka MAP44 345 4.41 120 10
Prion inhibition 2WVO_B ENEIEEVEDE Structure of the het-s n-terminal domain 222 5.00 184 10 2WVQ_B EIEIEEVEDE Structure of the het-s n-terminal domain. mutant d23a, p33h 207 5.28 171 10
Unknown function 2FDO_B FDADEDEIDEK Crystal structure of the conserved protein of unknown function AF2331 from Archaeoglobus fulgidus DSM 4304 89 4.25 59 11 reveals a new type of alpha/beta fold 2PRV_A EAKDDWDEDEDWD Crystal structure of an uncharacterized protein (YOBK, BSU18990) from Bacillus subtilis at 1.30 Å resolution 151 4.02 138 13 1IZM_A GYDEDDNEEELAE Structure of YGFB from Haemophilus influenzae (HI0817), a conserved hypothetical protein 168 3.73 136 13 1XAX_A DHIEDDEAEEMES NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae 144 4.06 121 13 4KLK_A RDGDEEDTEERPE Phage-related protein DUF2815 from Enterococcus faecalis 161 4.81 64 13 2D4R_D WLEEEEWDDENL Crystal structure of TTHA0849 from Thermus thermophilus HB8 144 5.00 60 12 1IHN_B EEELEELLEE X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 Å resolution reveals a 111 6.50 49 10 novel tertiary protein fold