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1 3 6-Mer Hemocyanin from Cryoem and Amino Acid Sequence doi:10.1016/S0022-2836(02)01173-7 J. Mol. Biol. (2003) 325, 99–109 Quaternary Structure of the European Spiny Lobster (Palinurus elephas )13 6-mer Hemocyanin from cryoEM and Amino Acid Sequence Data Ulrich Meissner1*, Michael Stohr1, Kristina Kusche1 Thorsten Burmester1, Holger Stark2, J. Robin Harris1, Elena V. Orlova3 and Ju¨ rgen Markl1 1Institute of Zoology Arthropod hemocyanins are large respiratory proteins that are composed University of Mainz of up to 48 subunits (8 £ 6-mer) in the 75 kDa range. A 3D reconstruction Muellerweg 6, D-55099 Mainz of the 1 £ 6-mer hemocyanin from the European spiny lobster Palinurus Germany elephas has been performed from 9970 single particles using cryoelectron microscopy. An 8 A˚ resolution of the hemocyanin 3D reconstruction 2MPI for Biophysical Chemistry has been obtained from about 600 final class averages. Visualisation of Am Fassberg 11, D-37077 structural elements such as a-helices has been achieved. An amino acid Go¨ttingen, Germany sequence alignment shows the high sequence identity (.80%) of the 3Department of hemocyanin subunits from the European spiny lobster P. elephas and the Crystallography, Birkbeck American spiny lobster Panulirus interruptus. Comparison of the P. elephas College, University of London hemocyanin electron microscopy (EM) density map with the known Malet Street, London WC1E P. interruptus X-ray structure shows a close structural correlation, demon- 7HX, UK strating the reliability of both methods for reconstructing proteins. By molecular modelling, we have found the putative locations for the amino acid sequence (597–605) and the C-terminal end (654–657), which are absent in the available P. interruptus X-ray data. q 2002 Elsevier Science Ltd. All rights reserved Keywords: 3D-EM, cryoelectron microscopy (cryoEM); 3D reconstruction; *Corresponding author Crustacea; hemocyanin; quaternary structure Introduction depending on the species). Within the native Hc the subunit composition may be heterogeneous Hemocyanins (Hc) are the blue respiratory pro- and in several Hc multimers-specific structural teins of many arthropod and molluscan species.1,2 roles have been attributed to different subunits.1,4 For a molluscan hemocyanin didecamer, a 12 A˚ The structural hierarchy of arthropod hemo- resolution 3D structure has been obtained from cyanins, as assemblies of an increasing number of cryoelectron microscopic (cryoEM) data.3 Arthro- 1 £ 6-mers, has been correlated with functional pod hemocyanin quaternary structure is based on cooperativity during oxygen binding.5 This can the hexamer (1 £ 6-mer) that contains six ,75 kDa best be described by the nesting model.6,7,8 subunits. Each subunit binds reversibly a dioxygen Arthropod hemocyanins achieve Hill coefficients molecule between two histidine-chelated Cu(I) (a measure of cooperativity) of up to ten and ions. In many species, hemocyanin hexamers therefore provide useful molecular models for the associate to form higher molecular mass multimers study of structure–function relationships of high (i.e. 2 £ 6-mer, 4 £ 6-mer, 6 £ 6-mer and 8 £ 6-mer, molecular mass oligomeric proteins.1,2 In recent years, many arthropod hemocyanin sequences have been determined and compared,9,10 Abbreviations used: PelHc, P. elephas hemocyanin; and X-ray structures of hemocyanin subunits PinHc, P. interruptus hemocyanin; Hc, hemocyanin; from a chelicerate (the horse shoe crab Limulus cryoEM, cryoelectron microscopy; CTF, contrast transfer polyphemus ) and a crustacean (the spiny lobster function; RFA, reference-free alignment; MSA, multi- 11,12 variate statistical analysis; MRA, multi-reference Panulirus interruptus ) are available. The under- alignment. standing of conformational changes during coop- E-mail address of the corresponding author: erative interactions requires knowledge of the [email protected] high-resolution quaternary structure rather than 0022-2836/03/$ - see front matter q 2002 Elsevier Science Ltd. All rights reserved 100 Quaternary Structure of Spiny Lobster Hemocyanin Figure 1. Sequence alignment of spiny lobster hemocyanin subunits. PelHc1 to PelHc3, the P. elephas hemocyanin subunits 1–3 (a-type); PinHca and PinHcb, the P. interruptus hemocyanin subunits a and b (both a-type). The conserved residues are shaded in grey, the copper-binding histidine residues are white on a black background. The secondary structure elements are displayed as derived from the PinHc.11,52 a, a-helices; b, b-sheets; p , residues not included in PinHc PDB-file;11 s, disulphide bridges; CHO, carbohydrate. The g-type subunit of PinHc is not displayed. that of subunit arrangement alone. This has folding, the correspondence between X-ray struc- been provided by X-ray crystallography for ture and single particle cryoEM reconstruction has P. interruptus hemocyanin (PinHc).11,13,14 However, been achieved at the level of ,11 A˚ resolution.24 the Hc 1 £ 6-mer analysed in these studies was Moreover, functionally ATP-bound states of not the native molecule that contains three dif- GroEL have been solved in the sub-10 A˚ range ferent subunit types, but an in vitro reassembly using cryoEM images.25 product containing equal quantities of subunits a Here we report the structure of the 1 £ 6-mer and b. Moreover, high resolution X-ray data of hemocyanin of the European spiny lobster the deoxygenated 1 £ 6-mer is still lacking, and all Palinurus elephas at a resolution of 8 A˚ from attempts to crystallize arthropod hemocyanin cryoEM data. This structure has been compared multimers have failed. Electron microscopy (EM), with the known X-ray structure of the hemocyanin as an alternative approach, has produced low of the closely related species P. interruptus. resolution quaternary structures,15 – 21 but no high- resolution (sub-10 A˚ ) cryoEM data set of arthropod hemocyanin has been published to date. CryoEM followed by single particle analysis Results has become a standard method for determining Primary structure of P. elephas molecular structure at medium resolution.22 For hemocyanin (PelHc) several molecules, 3D reconstruction from EM data, where the X-ray structure is known, has Three slightly different hemocyanin subunit been used for analysing conformational changes.23 sequences were obtained from a hepatopancreas With GroEL, a chaperone responsible for protein cDNA library of P. elephas (named PelHc1 to Quaternary Structure of Spiny Lobster Hemocyanin 101 Figure 2. A representative cryo-electron micrograph of PelHc. The 1 £ 6-mer hemocyanin molecules are visible at low contrast in the vitreous ice near to focus. PelHc3 hereinafter; EMBL/GenBank accession Cryoelectron microscopy and 3D-analysis numbers AJ344361-AJ344363). The deduced pro- teins contain 656 (PelHc1 and PelHc2) and 657 Hemocyanin was purified from the hemolymph (PelHc3) amino acid residues, excluding the signal of P. elephas by size-exclusion chromatography. peptides (Figure 1). The three P. elephas subunits The purity of the samples was assessed by native differ at 25–38 amino acid positions (94.2–96.2% PAGE, SDS-PAGE and negative staining EM. identity; 97.0–98.3% similarity considering iso- Cryoelectron micrographs were recorded as functional amino acid replacements). A single described in Materials and Methods. A total of £ amino acid residue insertion was observed in 9970 1 6-mer PelHc particles were interactively PelHc3 between b-sheets 3D and 3E. Comparison selected from six electron micrographs (Figure 2). of three PelHc sequences with the two hemocyanin Defocus was evaluated for each negative and subunits a and b of P. interruptus hemocyanin results are shown in Table 1. Comparison of the (PinHca, PinHcb )26,27 shows that the sequences nominal instrumental defocus with that deter- of the two species differ at 119–131 amino acid mined from the micrographs demonstrated that it positions (80.0–81.9% identity; 91.6–92.4% was systematically shifted by ,0.9 mm. Images similarity) (Figure 1). Phylogenetic analyses show from each micrograph were individually corrected that all three of the P. elephas subunits and the for the phase contrast transfer function (CTF). P. interruptus a and b subunits belong to the a-type A reference-free alignment (RFA) was performed crustacean hemocyanin sub-family.4,9,28 for 5258 molecules extracted from two electron micrographs. The following classification by multi-variate statistical analysis (MSA) enabled us to obtain a first set of references for multi-reference alignment (MRA) and then to extract the first 20 Table 1. Distribution of single particle in micrographs classes for 3D analysis, including several top and evaluated defocus views, but mainly side views; top: b-angle ¼ 08, Micrograph Number of images Defocus (mm) side: b-angle ¼ 908; see Figure 3(b)). Re-projections of the first reconstruction were used for the 1 1203 1.6 2 3712 1.9 next round of MRA and MSA. Four iterations 3 1477 2.5 were performed, including both alignment with 4 748 2.6 classification and determination of angular orien- 5 1830 2.6 tation. During the refinement the number of 6 1000 2.9 Hc particles was progressively increased, to the 102 Quaternary Structure of Spiny Lobster Hemocyanin Comparison of the density maps of the X-ray structure of PinHc to the 3D cryo-TEM reconstruction of PelHc As shown in Figure 4, the two maps, displayed as sections, gives an initial indication of the close similarity of the two structures. In the majority of the sections, a nearly perfect match can be seen. Only the sections 31–33 and 67–69 show some differences in the densities, resulting from a few amino acid residues that are not resolved in the X-ray structure of PinHc (Figure 4(b)). These residues are displayed in green in Figure 8, below, for one subunit after manual fitting inside the cryoEM density map. In addition, the densities within sections 48–51 shown in Figure 4 differ in their distribution, though they have general features in common. Fitting of the X-ray structure of PinHc into the 3D cryoEM reconstruction of PelHc Using the computer program MOLREP, auto- matic 3D fitting of the X-ray structure of PinHc (1 £ 6-mer) to the cryoEM density map of PelHc (Figure 6) was performed.
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