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- EMDB-39598: cryo-EM structure of carboxysomal midi-shell: icosahedral assembl... -

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Basic information

Entry
Database: EMDB / ID: EMD-39598
Titlecryo-EM structure of carboxysomal midi-shell: icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
Map data
Sample
  • Complex: Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
    • Protein or peptide: Major carboxysome shell protein CsoS1A
    • Protein or peptide: Carboxysome assembly protein CsoS2B
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
KeywordsCarboxysome / shell / Icosahedron / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / viral translational frameshifting
Similarity search - Function
Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain ...Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Carboxysome assembly protein CsoS2B / Carboxysome shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang P / Li JX / Li TP / Li K / Ng PC / Wang SM / Chriscoli V / Basle A / Marles-Wright J / Zhang YZ / Liu LN
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32090109 China
CitationJournal: Sci Adv / Year: 2024
Title: Molecular principles of the assembly and construction of a carboxysome shell.
Authors: Peng Wang / Jianxun Li / Tianpei Li / Kang Li / Pei Cing Ng / Saimeng Wang / Vincent Chriscoli / Arnaud Basle / Jon Marles-Wright / Yu-Zhong Zhang / Lu-Ning Liu /
Abstract: Intracellular compartmentalization enhances biological reactions, crucial for cellular function and survival. An example is the carboxysome, a bacterial microcompartment for CO fixation. The ...Intracellular compartmentalization enhances biological reactions, crucial for cellular function and survival. An example is the carboxysome, a bacterial microcompartment for CO fixation. The carboxysome uses a polyhedral protein shell made of hexamers, pentamers, and trimers to encapsulate Rubisco, increasing CO levels near Rubisco to enhance carboxylation. Despite their role in the global carbon cycle, the molecular mechanisms behind carboxysome shell assembly remain unclear. Here, we present a structural characterization of α-carboxysome shells generated from recombinant systems, which contain all shell proteins and the scaffolding protein CsoS2. Atomic-resolution cryo-electron microscopy of the shell assemblies, with a maximal size of 54 nm, unveil diverse assembly interfaces between shell proteins, detailed interactions of CsoS2 with shell proteins to drive shell assembly, and the formation of heterohexamers and heteropentamers by different shell protein paralogs, facilitating the assembly of larger empty shells. Our findings provide mechanistic insights into the construction principles of α-carboxysome shells and the role of CsoS2 in governing α-carboxysome assembly and functionality.
History
DepositionMar 28, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39598.png

Downloads & links

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Map

FileDownload / File: emd_39598.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 500 pix.
= 530. Å		1.06 Å/pix.
x 500 pix.
= 530. Å		1.06 Å/pix.
x 500 pix.
= 530. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.9545407 - 3.4339168
Average (Standard dev.)0.0059005646 (±0.17828995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 530.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39598_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39598_half_map_2.map
Projections & Slices
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Sample components

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Entire : Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B...

EntireName: Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
Components
  • Complex: Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
    • Protein or peptide: Major carboxysome shell protein CsoS1A
    • Protein or peptide: Carboxysome assembly protein CsoS2B
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A

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Supramolecule #1: Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B...

SupramoleculeName: Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)

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Macromolecule #1: Major carboxysome shell protein CsoS1A

MacromoleculeName: Major carboxysome shell protein CsoS1A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 9.973478 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVTGIALG MIETRGLVPA IEAADAMTKA AEVRLVGRQF VGGGYVTVLV RGETGAVNAA VRAGADACER VGDGLVAAHI IARVHSEVE NILPKAPQA

UniProtKB: Major carboxysome shell protein CsoS1A

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Macromolecule #2: Carboxysome assembly protein CsoS2B

MacromoleculeName: Carboxysome assembly protein CsoS2B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 29.358428 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPFCTSTPEP EAQSTEQSLT CEGQIISGTS VDASDLVTGN EIGEQQLISG DAYVGAQQTG CLPTSPRFNQ TGNVQSMGFK NTNQPEQNF APGEVMPTDF SIQTPARSAQ NRITGNDIAP SGRITGPGML ATGLITGTPE FRHAARELVG SPQPMAMAMA N RNKAAQAP ...String:
MPFCTSTPEP EAQSTEQSLT CEGQIISGTS VDASDLVTGN EIGEQQLISG DAYVGAQQTG CLPTSPRFNQ TGNVQSMGFK NTNQPEQNF APGEVMPTDF SIQTPARSAQ NRITGNDIAP SGRITGPGML ATGLITGTPE FRHAARELVG SPQPMAMAMA N RNKAAQAP VVQPEVVATQ EKPELVCAPR SDQMDRVSGE GKERCHITGD DWSVNKHITG TAGQWASGRN PSMRGNARVV ET SAFANRN VPKPEKPGSK ITGSSGNDTQ GSLITYSGGA RG

UniProtKB: Carboxysome assembly protein CsoS2B

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Macromolecule #3: Carboxysome shell vertex protein CsoS4A

MacromoleculeName: Carboxysome shell vertex protein CsoS4A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 8.900287 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKIMQVEKTL VSTNRIADMG HKPLLVVWEK PGAPRQVAVD AIGCIPGDWV LCVGSSAARE AAGSKSYPSD LTIIGIIDQW NGE

UniProtKB: Carboxysome shell vertex protein CsoS4A

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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
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8b12

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40177
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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