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Greber Etal Nature 2013 Suppl Research Collection Journal Article Architecture of the large subunit of the mammalian mitochondrial ribosome Author(s): Greber, Basil J.; Boehringer, Daniel; Leitner, Alexander; Bieri, Philipp; Voigts-Hoffmann, Felix; Erzberger, Jan P.; Leibundgut, Marc; Aebersold, Ruedi; Ban, Nenad Publication Date: 2014-01-23 Permanent Link: https://doi.org/10.3929/ethz-b-000080459 Originally published in: Nature 505(7484), http://doi.org/10.1038/nature12890 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Supplementary Online Material for Architecture of the Large Subunit of the Mammalian Mitochondrial Ribosome Basil J. Greber*, Daniel Boehringer*, Alexander Leitner, Philipp Bieri, Felix Voigts-Hoffmann, Jan P. Erzberger, Marc Leibundgut, Ruedi Aebersold†, and Nenad Ban† † Correspondence to: [email protected] (NB); [email protected] (RA) * These authors contributed equally to this work This file contains: Supplementary Tables 1 to 3 Supplementary Information References 1 Supplementary Table 1 – Summary of protein components in the 39S subunit model. MW, molecular weight; aa amino acids; RP, ribosomal protein. Modeling MRP † † Bacterial † MW Sequence Chain Modeled Coverage template Bacterial Protein* size RP size Comments (kDa) accession code ID residues (%) (PDB ID, homolog* (aa) (aa) chain ID) with homologs in bacterial ribosomes MRPL1 304 34.3 AK349766.1 L1 229 MRPL2 306 33.2 NP_001171996.1 D 75-274 65 3V2D (D) L2 276 MRPL3 399 43.6 XP_001925073.2 E 148-355 52 3V2D (E) L3 206 residues 59-77 MRPL4 294 33.2 XP_003123269.2 F 59-282 76 3V2D (F) L4 210 and 274-282 UNK‡ MRPL9 268 30.3 XP_003355223.1 I 94-150 21 3V2D (I) L9 148 MRPL10 262 29.4 XP_003131579.1 L10 130 MRPL11 192 20.8 XP_003122536.1 L11 147 MRPL12 198 21.2 AK234571.1 L7/L12 125 MRPL13 178 20.6 NP_001230344.1 N 1-147 82 3V2D (N) L13 140 MRPL14 145 15.9 XP_001929599.1 O 32-145 79 3V2D (O) L14 122 residues 9-21 MRPL15 296 33.4 NP_001230457.1 P 9-177 57 3V2D (P) L15 150 UNK‡ residues 192- MRPL16 251 28.6 NP_001231896.1 Q 55-208 61 3V2D (Q) L16 141 208 UNK‡ MRPL17 169 19.2 NP_001231309.1 R 9-128 71 3V2D (R) L17 118 MRPL18 180 20.5 XP_001928391.1 S 79-172 52 3V2D (S) L18 112 MRPL19 292 33.4 XP_003354803.1 T 87-205 41 3V2D (T) L19 146 residues 125- MRPL20 149 17.5 XP_003127555.3 U 10-132 82 3V2D (U) L20 118 132 UNK‡ residues 204- MRPL21 209 23.1 XP_003122473.3 V 99-207 52 3V2D (V) L21 101 207 UNK‡ residues 180- MRPL22 210 24.3 AK392578.1 W 70-203 63 3V2D (W) L22 113 203 UNK‡ residues 22-35 MRPL23 150 17.6 AK392218.1 X 22-108 57 3V2D (X) L23 96 and 104-108 UNK‡ MRPL24 216 24.9 NP_001231377.1 Y 53-155 48 3V2D (Y) L24 110 residues 105- MRPL27 148 15.9 XP_003131628.3 0 38-135 51 3V2D (0) L27 85 126 not modelled MRPL28 256 30.1 XP_003124744.1 1 82-139 23 3V2D (1) L28 98 MRPL47 252 30.0 XP_003132595.1 2 86-161 30 1R73 (A) L29 72 MRPL30 161 18.5 XP_003124942.1 3 65-123 37 3V2D (3) L30 60 Zn2+ binding; 79-146 MRPL32 188 21.5 XP_003360256.1 5 36 3V2D (5) L32 60 residues 127- + Zn 500 146 UNK‡ MRPL33 65 7.5 XP_003125332.1 6 13-60 74 3V2D (6) L33 54 MRPL34 95 10.8 AW415886.1 7 53-95 45 3V2D (7) L34 49 MRPL35 188 21.5 XP_003124984.1 8 103-162 32 3V2D (8) L35 65 64-99 2+ MRPL36 100 10.8 XP_003134214.1 9 36 3V2D (9) L36 37 Zn binding + Zn 500 without homologs in bacterial ribosomes MRPL37 423 47.9 AK237653.1 MRPL38 380 44.6 XP_003131236.1 b 145-336 51 2QYQ (J) PEBP-like fold§ tRNA synthetase MRPL39 334 38.5 XM_003132745.3 c 34-325 88 1QF6 (A) domain like§ residues 34-65 UNK‡ 2 Supplementary Table 1 (continued) Modeling MRP † † Bacterial MW Sequence Chain Modeled Coverage template Bacterial Protein* size† RP size Comments (kDa) accession code ID residues (%) (PDB ID, homolog* (aa) (aa) chain ID) without homologs in bacterial ribosomes MRPL40 206 24.0 NP_001230488.1 MRPL41 135 15.0 AW787117.1 MRPL42 142 16.7 AY609966.1 MRPL43 159 17.7 XP_003483589.1 thioredoxin like§ RNase III domain- MRPL44 332 37.5 NP_001230334.1 h 35-306 82 1O0W (B) like§ residues 35- 66 UNK§ MRPL45 306 35.3 AK232067.1 i 104-264 52 2CW9 (G) cystatin-like§ MRPL46 279 32.2 XP_003121908.1 nudix hydrolase§ MRPL48 212 23.7 XP_003129695.2 ferredoxin-like§ MRPL49 166 18.9 NP_001231942.1 l 91-166 45 2XZN (Z) eIF1-like§ MRPL50 159 18.3 XP_003122091.1 ACP-like§ MRPL51 123 14.2 I3LJG7 (Uniprot) residues 58-113 MRPL52 124 13.8 NP_001172080.1 o 58-113 45 - UNK‡ MRPL53 112 12.0 XM_003124989.1 thioredoxin-like§ MRPL54 138 15.9 XP_003123104.1 MRPL55 126 15.1 NP_001231893.1 β-lactamase/ MRPL56 556 61.8 NP_001230291.1 transpeptidase- like§ MRPL57 homeodomain- 102 12.0 AK347505.1 (MRP63) like§ peptidyl-tRNA MRPL58 hydrolase§ 205 23.5 NP_001231224.1 u 67-163 44 1J26 (A) (ICT1) residues 86-92 not modeled MRPL59 222 25.8 XP_003123387.1 (CRIF1) 5 α- unassigned α- helices helices of dimeric UNK§ v, w (91 aa) or pseudo dimeric each protein fold‡ 21 α- unassigned α- UNK§ z helices helices‡ (426 aa) 15-99 of unassigned UNK§ x 1S3A (A) template thioredoxin fold‡ * Nomenclature according to the ribosomal protein gene database 1. † Length, molecular weight and sequence coverage are calculated based on the full-length protein sequence (i.e. including putative mitochondrial targeting peptides). ‡ Unassigned residues were modeled as poly-serine and deposited as UNK. § Fold predicted by the Phyre2 protein fold recognition server 2. 3 Supplementary Table 2 – Overview of statistically significant hits for inter- protein chemical crosslinks of 39S subunit proteins obtained from CX-MS experiments using S. scrofa 39S subunits and B. taurus 55S mitoribosomes. Residue 1 Residue 2 Organism MRPL11 K13 MRPL53 K14 S. scrofa MRPL11 K12 MRPL53 K14 S. scrofa MRPL22 K54 MRPL24 K100 S. scrofa MRPL38 K274 MRPL52 K111 S. scrofa MRPL28 K12 MRPL37 K40 S. scrofa MRPL38 K85 MRPL52 K105 S. scrofa MRPL3 K330 MRPL19 K97 S. scrofa MRPL9 K81 MRPL28 K51 S. scrofa MRPL22 K54 MRPL24 K100 S. scrofa MRPL1 K297 CRIF1 K113 S. scrofa ICT1 K197 MRPL18 K114 S. scrofa MRPL38 K305 MRPL52 K105 S. scrofa MRPL38 K85 MRPL52 K105 S. scrofa MRPL20 K26 MRPL44 K43 S. scrofa MRPL9 K61 MRPL28 K51 S. scrofa MRPL38 K85 MRPL52 K98 S. scrofa ICT1 K93 MRPL49 K158 S. scrofa ICT1 K165 MRPL19 K227 S. scrofa MRPL12 K142 MRPL53 K14 S. scrofa MRPL11-1/-2 K51/K25 * MRPL12 K183 S. scrofa MRPL46 K100 MRPL40 K97 S. scrofa MRPL30 K44 MRPL16 K238 S. scrofa MRPL24 K32 MRPL45 K62 S. scrofa MRPL45 K62 MRPL24 K100 S. scrofa MRPL23 K115 MRPL45 K54 S. scrofa MRPL12 K138 MRPL53 K14 S. scrofa MRPL38 K85 MRPL52 K105 S. scrofa MRPL53 K105 MRPL11 K13 S. scrofa MRPL38 K305 MRPL52 K107 S. scrofa MRPL10 K132 MRPL53 K25 S. scrofa MRPL47 K136 MRPL9 K81 S. scrofa MRPL38 K305 MRPL52 K111 S. scrofa MRPL15 K249 ICT1 K66 S. scrofa MRPL45 K288 MRPL32 K132 S. scrofa MRPL12 K125 MRPL53 K14 S. scrofa * depending on isoform 4 Supplementary Table 2 (continued) Residue 1 Residue 2 Organism ICT1 K198 MRPL18 K114 B. taurus MRPL53 K105 MRPL11 K13 B. taurus MRPL22 K48 MRPL24 K100 B. taurus MRPL12 K142 MRPL11 K13 B. taurus MRPL47 K164 MRPL28 K221 B. taurus MRPL11 K13 MRPL12 K138 B. taurus ICT1 K66 MRPL15 K239 B. taurus MRPL9 K81 MRPL28 K55 B. taurus MRPL39 K123 MRPL45 K302 B. taurus MRPL37 K40 MRPL28 K150 B. taurus MRPL9 K81 MRPL28 K51 B. taurus MRPL3 K279 MRPL19 K97 B. taurus MRPL10 K132 MRPL53 K25 B. taurus MRPL45 K302 MRPL39 K65 B. taurus MRPL16 K188 MRPL1 K71 B. taurus MRPL53 K41 MRPL11 K13 B. taurus MRPL22 K48 MRPL24 K100 B. taurus MRPL42 K99 MRPL39 K201 B. taurus MRPL37 K40 MRPL2 K71 B. taurus MRPL10 K57 MRPL57 K32 B. taurus MRPL45 K177 MRPL22 K48 B. taurus MRPL53 K105 MRPL11 K13 B. taurus MRPL12 K138 MRPL10 K162 B. taurus MRPL53 K41 MRPL36 K90 B. taurus MRPL12 K142 MRPL10 K162 B. taurus MRPL11 K106 MRPL16 K116 B. taurus MRPL11 K106 MRPL54 K106 B. taurus ICT1 K47 CRIF1 K113 B. taurus ICT1 K94 MRPL49 K158 B. taurus MRPL53 K105 MRPL12 K138 B. taurus MRPL32 K143 MRPL45 K302 B. taurus MRPL9 K158 MRPL1 K71 B. taurus MRPL47 K74 MRPL41 K69 B. taurus MRPL9 K207 CRIF1 K113 B. taurus 5 Supplementary Table 3 – Crosslink data supporting our assignment of the localization of mitoribosomal-specific proteins. Mr, theoretical molecular mass; m/z, experimentally determined mass-to-charge ratio; Id score, identification score calculated by xQuest. Peptides Protein/ Protein/ Mr m/z Id Residue Residue (Da) Score Central Protuberance * FAFLLFKQDK-NALKSK-a7-b4 MRPL38 MRPL52 2053.169 685.397 33.44 K274 K111 EHFGEESGPKDR- MRPL38 MRPL52 2612.243 654.069 31.71 LQEEEGKQK-a10-b7 K85 K105 TFHTFDFYKK-LQEEEGKQK- MRPL38 MRPL52 2558.273 512.662 30.39 a9-b7 K305 K105 EHFGEESGPKDRVDIGLPPPK- MRPL38 MRPL52 3528.786 706.765 30.36 LQEEEGKQK-a10-b7 K85 K105 EHFGEESGPKDR- MRPL38 MRPL52 2869.344 574.877 30.04 QQEKLQEEEGK-a10-b4 K85 K98 TYREHFGEESGPKDR- MRPL38 MRPL52 3032.451 607.498 26.26 LQEEEGKQK-a13-b7 K85 K105 TFHTFDFYKK-QKNALK-a9-b2 MRPL38 MRPL52 2171.149 543.795 26.13 K305 K107 TFHTFDFYKK-NALKSK-a9-b4 MRPL38 MRPL52 2130.124 533.539 25.75 K305 K111 Placement of ICT1† Sus scrofa ISSAIKTSR-KHLYSTR-a6-b1 ICT1 MRPL18 2003.12 668.714 30.40 K197 K114 SSGPGGQNVNKVNSK- ICT1 MRPL49 3347.718 837.937 29.14 GYFDQQLKAWLLEK-a11-b8 K93 K158 DMIAEASQPAKEPSR- ICT1 MRPL19 3150.672 788.676 29.09 VKMKPKPWSKR-a11-b6 K165 K227 KYGYVLPDITKDELFK- MRPL15 ICT1 3731.94 933.993 25.74 LPDDAKQANDIPVDR-a11-b6 K249 K66 Bos taurus INSAIKTSR-KHLYSTK-a6-b1 ICT1 MRPL18 2002.121 668.382 34.98 K198 K114 VPGDAKQGNDDIPVDR- ICT1 MRPL15 2533.332 845.452 31.45 LELAKK-a6-b5 K66 K239 SSGPGGQNVNKVNSK- ICT1 MRPL49 3347.717 837.937 27.45 GYFDQQLKAWLLEK-a11-b8
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