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- PDB-8yve: cryo-EM structure of carboxysomal midi-shell: icosahedral assembl... -

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Basic information

Entry
Database: PDB / ID: 8yve
Titlecryo-EM structure of carboxysomal midi-shell: icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
Components
  • Carboxysome assembly protein CsoS2B
  • Carboxysome shell vertex protein CsoS4A
  • Major carboxysome shell protein CsoS1A
KeywordsSTRUCTURAL PROTEIN / Carboxysome / shell / Icosahedron
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang, P. / Li, J.X. / Li, T.P. / Li, K. / Ng, P.C. / Wang, S.M. / Chriscoli, V. / Basle, A. / Marles-Wright, J. / Zhang, Y.Z. / Liu, L.N.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A
C: Major carboxysome shell protein CsoS1A
D: Major carboxysome shell protein CsoS1A
E: Major carboxysome shell protein CsoS1A
F: Major carboxysome shell protein CsoS1A
N: Major carboxysome shell protein CsoS1A
R: Major carboxysome shell protein CsoS1A
X: Carboxysome assembly protein CsoS2B
v: Carboxysome shell vertex protein CsoS4A


Theoretical massNumber of molelcules
Total (without water)118,04710
Polymers118,04710
Non-polymers00
Water00
1
A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A
C: Major carboxysome shell protein CsoS1A
D: Major carboxysome shell protein CsoS1A
E: Major carboxysome shell protein CsoS1A
F: Major carboxysome shell protein CsoS1A
N: Major carboxysome shell protein CsoS1A
R: Major carboxysome shell protein CsoS1A
X: Carboxysome assembly protein CsoS2B
v: Carboxysome shell vertex protein CsoS4A
x 60


Theoretical massNumber of molelcules
Total (without water)7,082,792600
Polymers7,082,792600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A
C: Major carboxysome shell protein CsoS1A
D: Major carboxysome shell protein CsoS1A
E: Major carboxysome shell protein CsoS1A
F: Major carboxysome shell protein CsoS1A
N: Major carboxysome shell protein CsoS1A
R: Major carboxysome shell protein CsoS1A
X: Carboxysome assembly protein CsoS2B
v: Carboxysome shell vertex protein CsoS4A
x 5


  • icosahedral pentamer
  • 590 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)590,23350
Polymers590,23350
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A
C: Major carboxysome shell protein CsoS1A
D: Major carboxysome shell protein CsoS1A
E: Major carboxysome shell protein CsoS1A
F: Major carboxysome shell protein CsoS1A
N: Major carboxysome shell protein CsoS1A
R: Major carboxysome shell protein CsoS1A
X: Carboxysome assembly protein CsoS2B
v: Carboxysome shell vertex protein CsoS4A
x 6


  • icosahedral 23 hexamer
  • 708 kDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)708,27960
Polymers708,27960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major carboxysome shell protein CsoS1A


Mass: 9973.478 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS1A, csoS1, Hneap_0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P45689
#2: Protein Carboxysome assembly protein CsoS2B / Carboxysome assembly protein CsoS2-C


Mass: 29358.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS2, Hneap_0920 / Production host: Escherichia coli (E. coli) / References: UniProt: O85041
#3: Protein Carboxysome shell vertex protein CsoS4A


Mass: 8900.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS4A, orfA, Hneap_0918 / Production host: Escherichia coli (E. coli) / References: UniProt: O85043
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Carboxysomal midi-shell:icosahedral assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40177 / Symmetry type: POINT

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