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Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus

Nature Plants volume 10, pages 661–672 (2024)Cite this article

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Abstract

Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant ‘outside-in’ assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.

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Fig. 1: CsoSCA phylogenetic tree and gene organization of the cso operons among proteobacteria and α-cyanobacteria.
Fig. 2: Biochemical characterization of the α-carboxysome from Prochlorococcus MED4.
Fig. 3: Structure and assembly pattern of the icosahedral-like shell of the Prochlorococcus α-carboxysome.
Fig. 4: Structure of the scaffolding protein CsoS2 and its pattern of binding to the inner surface of the shell.
Fig. 5: Multivalent interactions between CsoS2 and the shell.
Fig. 6: Internal organization of RuBisCO within the Prochlorococcus α-carboxysome.
Fig. 7: An updated concomitant model for α-carboxysome assembly.

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Data availability

All cryo-EM maps have been deposited at the Electron Microscopy Data Bank (EMDB). The accession codes are as follows: shell vertex with C5 symmetry, EMD-37902; intact shell with icosahedral symmetry, EMD-38544; internal RuBisCOs with icosahedral symmetry, EMD-38543; and intact α-carboxysome with icosahedral symmetry, EMD-37903. The model of the shell vertex has been deposited to the Protein Data Bank under the accession code 8WXB. Mass spectroscopy data are deposited on Figshare at https://doi.org/10.6084/m9.figshare.25239463.v2 (ref. 67). The consecutive genes were blasted and retrieved from the KEGG database (https://www.kegg.jp/kegg/). Source data are provided with this paper.

References

  1. Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658 (2011).

    Article  CAS  PubMed  Google Scholar 

  2. Bar-On, Y. M. & Milo, R. The global mass and average rate of rubisco. Proc. Natl Acad. Sci. USA 116, 4738–4743 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Erb, T. J. & Zarzycki, J. A short history of RubisCO: the rise and fall (?) of Nature’s predominant CO2 fixing enzyme. Curr.Opin. Biotechnol. 49, 100–107 (2018).

    Article  CAS  PubMed  Google Scholar 

  4. Whitney, S. M., Houtz, R. L. & Alonso, H. Advancing our understanding and capacity to engineer nature’s CO2-sequestering enzyme, Rubisco. Plant Physiol. 155, 27–35 (2011).

    Article  CAS  PubMed  Google Scholar 

  5. Badger, M. R. & Price, G. D. CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution. J. Exp. Bot. 54, 609–622 (2003).

    Article  CAS  PubMed  Google Scholar 

  6. Kerfeld, C. A. & Melnicki, M. R. Assembly, function and evolution of cyanobacterial carboxysomes. Curr. Opin. Plant Biol. 31, 66–75 (2016).

    Article  CAS  PubMed  Google Scholar 

  7. Liu, L. N. Advances in the bacterial organelles for CO2 fixation. Trends Microbiol. 30, 567–580 (2022).

    Article  CAS  PubMed  Google Scholar 

  8. Price, G. D., Badger, M. R., Woodger, F. J. & Long, B. M. Advances in understanding the cyanobacterial CO2-concentrating-mechanism (CCM): functional components, Ci transporters, diversity, genetic regulation and prospects for engineering into plants. J. Exp. Bot. 59, 1441–1461 (2008).

    Article  CAS  PubMed  Google Scholar 

  9. Kerfeld, C. A., Aussignargues, C., Zarzycki, J., Cai, F. & Sutter, M. Bacterial microcompartments. Nat. Rev. Microbiol. 16, 277–290 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Sutter, M., Melnicki, M. R., Schulz, F., Woyke, T. & Kerfeld, C. A. A catalog of the diversity and ubiquity of bacterial microcompartments. Nat. Commun. 12, 3809 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Rae, B. D., Long, B. M., Badger, M. R. & Price, G. D. Functions, compositions, and evolution of the two types of carboxysomes: polyhedral microcompartments that facilitate CO2 fixation in cyanobacteria and some proteobacteria. Microbiol. Mol. Biol. Rev. 77, 357–379 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Dou, Z. et al. CO2 fixation kinetics of Halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2. J. Biol. Chem. 283, 10377–10384 (2008).

    Article  CAS  PubMed  Google Scholar 

  13. Faulkner, M. et al. Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein. Sci. Rep. 10, 17501 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kinney, J. N., Axen, S. D. & Kerfeld, C. A. Comparative analysis of carboxysome shell proteins. Photosynth. Res. 109, 21–32 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Liu, X. Y. et al. Structures of cyanobacterial bicarbonate transporter SbtA and its complex with PII-like SbtB. Cell Discov. 7, 63 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Wang, C. et al. Structural mechanism of the active bicarbonate transporter from cyanobacteria. Nat. Plants 5, 1184–1193 (2019).

    Article  CAS  PubMed  Google Scholar 

  17. Long, B. M., Forster, B., Pulsford, S. B., Price, G. D. & Badger, M. R. Rubisco proton production can drive the elevation of CO2 within condensates and carboxysomes. Proc. Natl Acad. Sci. USA 118, e2014406118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Cabello-Yeves, P. J. et al. ɑ-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. ISME J. 16, 2421–2432 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Whitehead, L., Long, B. M., Price, G. D. & Badger, M. R. Comparing the in vivo function of alpha-carboxysomes and beta-carboxysomes in two model cyanobacteria. Plant Physiol. 165, 398–411 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Long, B. M., Badger, M. R., Whitney, S. M. & Price, G. D. Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA. J. Biol. Chem. 282, 29323–29335 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Kinney, J. N., Salmeen, A., Cai, F. & Kerfeld, C. A. Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly. J. Biol. Chem. 287, 17729–17736 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Sun, H. et al. Complex structure reveals CcmM and CcmN form a heterotrimeric adaptor in beta-carboxysome. Protein Sci. 30, 1566–1576 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Cai, F. et al. Advances in understanding carboxysome assembly in Prochlorococcus and Synechococcus implicate CsoS2 as a critical component. Life 5, 1141–1171 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Oltrogge, L. M. et al. Multivalent interactions between CsoS2 and Rubisco mediate alpha-carboxysome formation. Nat. Struct. Mol. Biol. 27, 281–287 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Faulkner, M. et al. Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes. Nanoscale 9, 10662–10673 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Huang, F. et al. Rubisco accumulation factor 1 (Raf1) plays essential roles in mediating Rubisco assembly and carboxysome biogenesis. Proc. Natl Acad. Sci. USA 117, 17418–17428 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wang, H. et al. Rubisco condensate formation by CcmM in beta-carboxysome biogenesis. Nature 566, 131–135 (2019).

    Article  CAS  PubMed  Google Scholar 

  28. Cameron, J. C., Wilson, S. C., Bernstein, S. L. & Kerfeld, C. A. Biogenesis of a bacterial organelle: the carboxysome assembly pathway. Cell 155, 1131–1140 (2013).

    Article  CAS  PubMed  Google Scholar 

  29. Roberts, E. W., Cai, F., Kerfeld, C. A., Cannon, G. C. & Heinhorst, S. Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D. J. Bacteriol. 194, 787–795 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Oltrogge, L. M., Chen, A. W., Chaijarasphone, T., Turnšek, J. B. & Savage, D. F. α-carboxysome size is controlled by the disordered scaffold protein CsoS2. Biochemistry 63, 219–229 (2024).

  31. Turnšek, J. B., Oltrogge, L. M. & Savage, D. F. Conserved and repetitive motifs in an intrinsically disordered protein drive α-carboxysome assembly. Preprint at bioRxiv https://doi.org/10.1101/2023.07.08.548221 (2023).

  32. Ni, T. et al. Intrinsically disordered CsoS2 acts as a general molecular thread for alpha-carboxysome shell assembly. Nat. Commun. 14, 5512 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ni, T. et al. Structure and assembly of cargo Rubisco in two native alpha-carboxysomes. Nat. Commun. 13, 4299 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Evans, S. L. et al. Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact alpha-carboxysome. Structure 31, 677–688 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Metskas, L. A. et al. Rubisco forms a lattice inside alpha-carboxysomes. Nat. Commun. 13, 4863 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Xia, L. Y. et al. Molecular basis for the assembly of RuBisCO assisted by the chaperone Raf1. Nat. Plants 6, 708–717 (2020).

    Article  CAS  PubMed  Google Scholar 

  37. Li, Q., Jiang, Y. L., Xia, L. Y., Chen, Y. & Zhou, C. Z. Structural insights into cyanobacterial RuBisCO assembly coordinated by two chaperones Raf1 and RbcX. Cell Discov. 8, 93 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Tan, Y. Q. et al. Structure of a minimal alpha-carboxysome-derived shell and its utility in enzyme stabilization. Biomacromolecules 22, 4095–4109 (2021).

    Article  CAS  PubMed  Google Scholar 

  39. Sutter, M. et al. Structure of a synthetic beta-carboxysome shell. Plant Physiol. 181, 1050–1058 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Sutter, M., Greber, B., Aussignargues, C. & Kerfeld, C. A. Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell. Science 356, 1293–1297 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ulloa, O. et al. The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean. Proc. Natl Acad. Sci. USA 118, e2025638118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Zhu, D. et al. Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions. Nat. Commun. 9, 1552 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Partensky, F., Hess, W. R. & Vaulot, D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63, 106–127 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Cai, L., Li, H., Deng, J., Zhou, R. Q. & Zeng, Q. Biological interactions with Prochlorococcus: implications for the marine carbon cycle. Trends Microbiol. 32, 280–291 (2024).

  45. Cai, F. et al. The structure of CcmP, a tandem bacterial microcompartment domain protein from the beta-carboxysome, forms a subcompartment within a microcompartment. J. Biol. Chem. 288, 16055–16063 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Tanaka, S. et al. Atomic-level models of the bacterial carboxysome shell. Science 319, 1083–1086 (2008).

    Article  CAS  PubMed  Google Scholar 

  47. Wheatley, N. M., Sundberg, C. D., Gidaniyan, S. D., Cascio, D. & Yeates, T. O. Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the ɑ-carboxysome. J. Biol. Chem. 289, 7973–7981 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Sun, Y. et al. Decoding the absolute stoichiometric composition and structural plasticity of alpha-carboxysomes. mBio 13, e0362921 (2022).

    Article  PubMed  Google Scholar 

  49. Liu, J., Xing, W. Y., Liu, B. & Zhang, C. C. Three-dimensional coordination of cell-division site positioning in a filamentous cyanobacterium. PNAS Nexus 2, pgac307 (2023).

    Article  PubMed  Google Scholar 

  50. Greber, B. J., Sutter, M. & Kerfeld, C. A. The plasticity of molecular interactions governs bacterial microcompartment shell assembly. Structure 27, 749–763 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Blikstad, C. et al. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc. Natl Acad. Sci. USA 120, e2308600120 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Chaijarasphong, T. et al. Programmed ribosomal frameshifting mediates expression of the alpha-carboxysome. J. Mol. Biol. 428, 153–164 (2016).

    Article  CAS  PubMed  Google Scholar 

  53. Iancu, C. V. et al. Organization, structure, and assembly of alpha-carboxysomes determined by electron cryotomography of intact cells. J. Mol. Biol. 396, 105–117 (2010).

    Article  CAS  PubMed  Google Scholar 

  54. Chen, T. et al. Engineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis. Nat. Commun. 14, 2118 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Li, T. et al. Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nat. Commun. 11, 5448 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Article  CAS  PubMed  Google Scholar 

  57. Moore, L. R. et al. Culturing the marine cyanobacterium Prochlorococcus. Limnol. Oceanogr. Methods 5, 353–362 (2007).

    Article  CAS  Google Scholar 

  58. Scheres, S. H. W. Amyloid structure determination in RELION-3.1. Acta Crystallogr. D 76, 94–101 (2020).

    Article  CAS  Google Scholar 

  59. Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  61. Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article  PubMed  Google Scholar 

  64. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  66. Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  PubMed  Google Scholar 

  67. Zhou, R. Proteomic analysis for freshly purified Prochlorococcus MED4 carboxysome was performed via Orbitrap Eclipse Tribrid Mass Spectrometry (Thermo Scientific). Figshare https://doi.org/10.6084/m9.figshare.25239463.v2 (2024).

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Acknowledgements

All cryo-EM datasets were collected at the Biological Cryo-EM Center at HKUST. This work was supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (http://www.cas.cn; Precision Seed Design and Breeding, grant no. XDA24020302, Y.-L.J.), the Research Grants Council of the Hong Kong Special Administrative Region, China (https://www.ugc.edu.hk; grant no. HKUST C6012-22GF, Q.Z.), the Environment and Conservation Fund (https://www.ugc.edu.hk; grant ECF project 128/2020, Q.Z.), the Strategic Priority Research Program of the Chinese Academy of Sciences (http://www.cas.cn; grant XDB37020301, C.-Z.Z.), and the National Natural Science Foundation of China (http://www.nsfc.gov.cn; grants 32241025 to C.-Z.Z. and 32171198 to Y.-L.J.), the Anhui Provincial Natural Science Foundation (http://kjt.ah.gov.cn; 2108085J14, Y.-L.J.) and the Key R&D Projects of Anhui Province (http://kjt.ah.gov.cn; 2022l07020034, Y.-L.J.). Y.-L.J. thanks the Youth Innovation Promotion Association of the Chinese Academy of Sciences for support (membership no. 2020452).

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  1. These authors contributed equally: Rui-Qian Zhou, Yong-Liang Jiang.

Authors and Affiliations

  1. Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China

    Rui-Qian Zhou, Haofu Li & Qinglu Zeng

  2. School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China

    Rui-Qian Zhou, Yong-Liang Jiang, Pu Hou, Wen-Wen Kong, Jia-Xin Deng, Yuxing Chen & Cong-Zhao Zhou

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Contributions

Y.-L.J., Q.Z, C.-Z.Z. and Y.C. conceived, designed and supervised this project. R.-Q.Z., H.L., W.-W.K. and J.-X.D. performed the Prochlorococcus growth experiment. R.-Q.Z. performed α-carboxysome purification, biochemical assays, cryo-EM sample preparation and data collection. Y.-L.J. and P.H. conducted cryo-EM data processing, structure determination and model building. Y.-L.J., R.-Q.Z., C.-Z.Z. and Q.Z. wrote and revised the manuscript with input from all authors. All authors discussed the data and read the manuscript.

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Correspondence to Yong-Liang Jiang, Cong-Zhao Zhou or Qinglu Zeng.

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Extended data

Extended Data Fig. 1 Fitting of the CsoS4A pentamer to the Cryo-EM map at the shell vertex.

The structure of CsoS4A pentamer is shown as a yellow cartoon with the N-terminal ten residues (labeled N-ter) colored red.

Extended Data Fig. 2 Overview of the distinct interfaces among hexamers and pentamers.

The structures of the hexamers (blue) and pentamers (yellow) are shown as cartoons, with a pictogram showing their location on the shell. The tilt angles of the hexamer-hexamer or hexamer-pentamer interfaces are labeled.

Extended Data Fig. 3 Multiple sequence alignment of the α-carboxysome (a) BMC-H and (b) BMC-P proteins.

The BMC-H and BMC-P sequences of twelve organisms that harbor α-carboxysomes were retrieved from the UniProt protein database. The KAA and ARPH motifs from BMC-H proteins and the interface residues from BMC-P proteins are labeled with blue and brown solid circles, respectively. The conserved His75 of BMC-H that binds to the V/L/ITG motif of CsoS2 is marked with a red triangle.

Extended Data Fig. 4 Local arrangement of CsoS2 subunits on the inner surface of the shell viewed from the (a) threefold and (b) twofold axes of the α-carboxysome shell.

The structures of the shell patches are shown as semitransparent cartoons, with each asymmetric unit colored differently. The structures of the long and short forms of CsoS2 are colored red and green, respectively. The three- and twofold axes of the α-carboxysome shell are indicated by black solid triangles and ovals, respectively. The positions that are vacant for CsoS2 binding are marked with four black circles in a.

Extended Data Fig. 5 A global view of the arrangement of CsoS2 subunits on the inner surface of the intact icosahedral-like shell viewed from the (a) threefold and (b) fivefold axes of the shell.

The structure of the icosahedral-like shell is shown as a semitransparent cartoon, with BMC-H hexamers and BMC-P pentamers colored blue and yellow, respectively. The structures of the long and short forms of CsoS2 are colored red and green, respectively. The twofold, threefold and fivefold axes of the α-carboxysome shell are indicated by black solid ovals, triangles and pentagons, respectively.

Extended Data Fig. 6 Structural comparison of the six M repeats of CsoS2.

The six M repeats are shown as cartoons and are colored differently, as shown on the right. A pair of cysteine residues in each of the M repeats is shown as sticks.

Extended Data Fig. 7 Surface representation of the CsoS1-CsoS2 interface.

a, Overall view of the conservation profile of the interface between the shell protein CsoS1 and the scaffolding protein CsoS2. The structures of CsoS1 and CsoS2 are shown in cartoon and surface, respectively. Coloring is by calculated amino acid conservation entropy (red, 100% conservation). b, Zoomed in view of the interface between β4 of the shell protein CsoS1 and the V/L/ITG motif of the scaffolding protein CsoS2. c, The sequence alignments were depicted using Weblogo. The sequence logo shows the conservation of the residues at the interface between CsoS1 and CsoS2.

Extended Data Fig. 8 Cartoon representation of CsoS2 subunits binding to an asymmetric unit of the icosahedral-like shell.

The CsoS1 hexamers, the CsoS4A pentamer, and the CsoS2 subunits are shown as cartoons and are colored blue, yellow, and red/green, respectively. The individual M and C repeats of CsoS2 are numbered sequentially.

Extended Data Fig. 9 The interaction of the C-terminus of CsoS2 binding to the CsoS4A pentamer.

The C3 region of CsoS2 and CsoS4A are shown as cartoons and are colored red and yellow, respectively. The detailed interaction networks are shown in the inset, with the interface residues shown as sticks.

Extended Data Fig. 10 Internal arrangement of RuBisCO within the outer and middle layers of a-carboxysomes.

a, Slab section of the overall density in the outer and middle layers of the α-carboxysome. Three RuBisCOs were fitted to the cryo-EM density and are labeled 1, 2, and 3. Two RuBisCOs from the outer layer are colored blue, whereas the third one from the middle layer is colored pink. b, c, Cartoon representations of two adjacent RuBisCOs forming lateral (b) or longitudinal (c) interfaces, shown as cartoons through the transparent surface.

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Supplementary Information

Supplementary Figs. 1–3, and Tables 1 and 2.

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Source data

Source Data Fig. 2

Unprocessed SDS–PAGE gel for Fig. 2b.

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Zhou, RQ., Jiang, YL., Li, H. et al. Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. Nat. Plants 10, 661–672 (2024). https://doi.org/10.1038/s41477-024-01660-9

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