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- EMDB-37902: Cryo-EM structure of the alpha-carboxysome shell vertex from Proc... -

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Basic information

Entry
Database: EMDB / ID: EMD-37902
TitleCryo-EM structure of the alpha-carboxysome shell vertex from Prochlorococcus MED4
Map data
Sample
  • Complex: The shell vertex of alpha-carboxysome
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Major carboxysome shell protein CsoS1
    • Protein or peptide: Carboxysome assembly protein CsoS2
Keywordsalpha-carboxysome / carbon fixation / PHOTOSYNTHESIS
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. ...Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
Carboxysome shell vertex protein CsoS4A / Carboxysome assembly protein CsoS2 / Major carboxysome shell protein CsoS1
Similarity search - Component
Biological speciesProchlorococcus sp. MED4 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsJiang YL / Zhou RQ / Zhou CZ / Zeng QL
Funding support China, Hong Kong, 5 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302 China
Chinese Academy of SciencesXDB37020301 China
The University Grants Committee, Research Grants Council (RGC)HKUST C6012-22GF Hong Kong
National Natural Science Foundation of China (NSFC)32241025 China
National Natural Science Foundation of China (NSFC)32171198 China
CitationJournal: Nat Plants / Year: 2024
Title: Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus.
Authors: Rui-Qian Zhou / Yong-Liang Jiang / Haofu Li / Pu Hou / Wen-Wen Kong / Jia-Xin Deng / Yuxing Chen / Cong-Zhao Zhou / Qinglu Zeng /
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- ...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.
History
DepositionOct 28, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37902.png

Downloads & links

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Map

FileDownload / File: emd_37902.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0057375845 - 0.014728917
Average (Standard dev.)0.00006225777 (±0.00056925573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions686686686
Spacing686686686
CellA=B=C: 727.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37902_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37902_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The shell vertex of alpha-carboxysome

EntireName: The shell vertex of alpha-carboxysome
Components
  • Complex: The shell vertex of alpha-carboxysome
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Major carboxysome shell protein CsoS1
    • Protein or peptide: Carboxysome assembly protein CsoS2

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Supramolecule #1: The shell vertex of alpha-carboxysome

SupramoleculeName: The shell vertex of alpha-carboxysome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Molecular weightTheoretical: 3.4 MDa

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Macromolecule #1: Carboxysome shell vertex protein CsoS4A

MacromoleculeName: Carboxysome shell vertex protein CsoS4A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Molecular weightTheoretical: 9.407823 KDa
SequenceString:
MLICKVLKPL VSTNRIPGFE HKHLQVVLDG SSNKVAVDAV GCKPGDWVIC VGSSAAREAA GSKSYPSDLT IVGIIDHWDP DSPKQIEV

UniProtKB: Carboxysome shell vertex protein CsoS4A

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Macromolecule #2: Major carboxysome shell protein CsoS1

MacromoleculeName: Major carboxysome shell protein CsoS1 / type: protein_or_peptide / ID: 2 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Molecular weightTheoretical: 10.050501 KDa
SequenceString:
MGIALGMIET RGLVPAIEAA DAMTKAAEVR LIGREFVGGG YVTVLVRGET GAVNAAVRAG ADACERVGDG LVAAHIIARP HREVEPALG NGDFLGQKD

UniProtKB: Major carboxysome shell protein CsoS1

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Macromolecule #3: Carboxysome assembly protein CsoS2

MacromoleculeName: Carboxysome assembly protein CsoS2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Molecular weightTheoretical: 82.006797 KDa
SequenceString: MSTKTSREIA LERRKAMSDG GKKAALHSSS TKDRVRSSQD INSTGATSSN KKVLTSPSKS NIPANKIARK STSSKLSSKE LGIERRKAM STHGKSAINS SDRTRTDVKS DIKVNKVIST EKPQALKDHN NNIKDNQVVK QNIKRRINQK RKPITNTSRD I VLARREAQ ...String:
MSTKTSREIA LERRKAMSDG GKKAALHSSS TKDRVRSSQD INSTGATSSN KKVLTSPSKS NIPANKIARK STSSKLSSKE LGIERRKAM STHGKSAINS SDRTRTDVKS DIKVNKVIST EKPQALKDHN NNIKDNQVVK QNIKRRINQK RKPITNTSRD I VLARREAQ SKHGKSASKQ NTSAASLARR GDPDLSSREI SQRVRELRSK TGSTSKQGNG KCRPCGPNKN GSKLNIADAS WK VGKSETD SGQTVTGTQA NRSLKTTGNE ASTCRTVTGT QYMGAEVTGQ FCQDKPKYKQ PIRASVTTTT SGNKVTGNEV GRS EKVTGD EPGTCKNLTG TEYISANQSK KYCGEVIKKP SKVMQSITTD GLKVSGSLPG RSSLVTGDES GSGKQLTGDQ YLGS EPSPK GKSFEKVGSY DTLNGNNVTG TGVGRSDYVT GNEYGSCKNL TGDEYIGSQQ YEKFCGSTPK PEARKVGLSL SSKSN LISG TMTGRSKIVT GDEPGSCKVL TGTPYAGLDQ INDNCNAEIA DDMKSRATVN SGNNSNARLT GLQPGIGGVM TGATKG SCK NLTGTPYIGG DQFLSNCETP PNDASYANQE KSASNSWKEF SVNSPSREKY SAKNTEGVTG NRYEDSSKIT GPFDMAE DK VTGTEQFRFE PNKNMTYKQK MKQEESQNID IPTDKKEPSK ITGEGQSAGN ITGDDWDRGD KVTGTEGVSA RKRNPSRA G FMGAMPPVDN KRNDETEKPD FLITGSSGNT RDGQLVTFSG GARG

UniProtKB: Carboxysome assembly protein CsoS2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold predicted model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28093
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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