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- PDB-8yvf: cryo-EM structure of carboxysomal midi-shell: assembly from CsoS4... -

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Basic information

Entry
Database: PDB / ID: 8yvf
Titlecryo-EM structure of carboxysomal midi-shell: assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T=9 Q=12)
Components
  • Carboxysome assembly protein CsoS2B
  • Carboxysome shell vertex protein CsoS4A
  • Major carboxysome shell protein CsoS1A
KeywordsSTRUCTURAL PROTEIN / Carboxysome / shell
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: 2.99 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
0: Major carboxysome shell protein CsoS1A
1: Carboxysome shell vertex protein CsoS4A
2: Major carboxysome shell protein CsoS1A
3: Major carboxysome shell protein CsoS1A
4: Carboxysome shell vertex protein CsoS4A
5: Major carboxysome shell protein CsoS1A
6: Major carboxysome shell protein CsoS1A
7: Major carboxysome shell protein CsoS1A
8: Major carboxysome shell protein CsoS1A
9: Major carboxysome shell protein CsoS1A
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
G: Major carboxysome shell protein CsoS1A
H: Major carboxysome shell protein CsoS1A
I: Major carboxysome shell protein CsoS1A
J: Major carboxysome shell protein CsoS1A
K: Major carboxysome shell protein CsoS1A
L: Major carboxysome shell protein CsoS1A
M: Major carboxysome shell protein CsoS1A
N: Major carboxysome shell protein CsoS1A
O: Major carboxysome shell protein CsoS1A
P: Major carboxysome shell protein CsoS1A
Q: Major carboxysome shell protein CsoS1A
R: Major carboxysome shell protein CsoS1A
S: Major carboxysome shell protein CsoS1A
T: Major carboxysome shell protein CsoS1A
U: Major carboxysome shell protein CsoS1A
V: Major carboxysome shell protein CsoS1A
W: Major carboxysome shell protein CsoS1A
X: Major carboxysome shell protein CsoS1A
Y: Major carboxysome shell protein CsoS1A
Z: Major carboxysome shell protein CsoS1A
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
g: Major carboxysome shell protein CsoS1A
h: Major carboxysome shell protein CsoS1A
i: Major carboxysome shell protein CsoS1A
j: Major carboxysome shell protein CsoS1A
k: Major carboxysome shell protein CsoS1A
l: Major carboxysome shell protein CsoS1A
m: Major carboxysome shell protein CsoS1A
n: Major carboxysome shell protein CsoS1A
o: Major carboxysome shell protein CsoS1A
p: Major carboxysome shell protein CsoS1A
q: Major carboxysome shell protein CsoS1A
r: Major carboxysome shell protein CsoS1A
s: Major carboxysome shell protein CsoS1A
t: Major carboxysome shell protein CsoS1A
u: Major carboxysome shell protein CsoS1A
v: Major carboxysome shell protein CsoS1A
w: Carboxysome shell vertex protein CsoS4A
x: Carboxysome shell vertex protein CsoS4A
y: Carboxysome shell vertex protein CsoS4A
z: Carboxysome shell vertex protein CsoS4A
A2: Carboxysome assembly protein CsoS2B
A3: Carboxysome assembly protein CsoS2B
A4: Carboxysome assembly protein CsoS2B
A5: Carboxysome assembly protein CsoS2B
A6: Carboxysome assembly protein CsoS2B
A7: Carboxysome assembly protein CsoS2B
X1: Carboxysome assembly protein CsoS2B
X2: Carboxysome assembly protein CsoS2B
A1: Major carboxysome shell protein CsoS1A


Theoretical massNumber of molelcules
Total (without water)856,75771
Polymers856,75771
Non-polymers00
Water00
1
0: Major carboxysome shell protein CsoS1A
1: Carboxysome shell vertex protein CsoS4A
2: Major carboxysome shell protein CsoS1A
3: Major carboxysome shell protein CsoS1A
4: Carboxysome shell vertex protein CsoS4A
5: Major carboxysome shell protein CsoS1A
6: Major carboxysome shell protein CsoS1A
7: Major carboxysome shell protein CsoS1A
8: Major carboxysome shell protein CsoS1A
9: Major carboxysome shell protein CsoS1A
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
G: Major carboxysome shell protein CsoS1A
H: Major carboxysome shell protein CsoS1A
I: Major carboxysome shell protein CsoS1A
J: Major carboxysome shell protein CsoS1A
K: Major carboxysome shell protein CsoS1A
L: Major carboxysome shell protein CsoS1A
M: Major carboxysome shell protein CsoS1A
N: Major carboxysome shell protein CsoS1A
O: Major carboxysome shell protein CsoS1A
P: Major carboxysome shell protein CsoS1A
Q: Major carboxysome shell protein CsoS1A
R: Major carboxysome shell protein CsoS1A
S: Major carboxysome shell protein CsoS1A
T: Major carboxysome shell protein CsoS1A
U: Major carboxysome shell protein CsoS1A
V: Major carboxysome shell protein CsoS1A
W: Major carboxysome shell protein CsoS1A
X: Major carboxysome shell protein CsoS1A
Y: Major carboxysome shell protein CsoS1A
Z: Major carboxysome shell protein CsoS1A
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
g: Major carboxysome shell protein CsoS1A
h: Major carboxysome shell protein CsoS1A
i: Major carboxysome shell protein CsoS1A
j: Major carboxysome shell protein CsoS1A
k: Major carboxysome shell protein CsoS1A
l: Major carboxysome shell protein CsoS1A
m: Major carboxysome shell protein CsoS1A
n: Major carboxysome shell protein CsoS1A
o: Major carboxysome shell protein CsoS1A
p: Major carboxysome shell protein CsoS1A
q: Major carboxysome shell protein CsoS1A
r: Major carboxysome shell protein CsoS1A
s: Major carboxysome shell protein CsoS1A
t: Major carboxysome shell protein CsoS1A
u: Major carboxysome shell protein CsoS1A
v: Major carboxysome shell protein CsoS1A
w: Carboxysome shell vertex protein CsoS4A
x: Carboxysome shell vertex protein CsoS4A
y: Carboxysome shell vertex protein CsoS4A
z: Carboxysome shell vertex protein CsoS4A
A2: Carboxysome assembly protein CsoS2B
A3: Carboxysome assembly protein CsoS2B
A4: Carboxysome assembly protein CsoS2B
A5: Carboxysome assembly protein CsoS2B
A6: Carboxysome assembly protein CsoS2B
A7: Carboxysome assembly protein CsoS2B
X1: Carboxysome assembly protein CsoS2B
X2: Carboxysome assembly protein CsoS2B
A1: Major carboxysome shell protein CsoS1A
x 10


Theoretical massNumber of molelcules
Total (without water)8,567,574710
Polymers8,567,574710
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation9
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D5 (2x5 fold dihedral))

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Components

#1: Protein ...
Major carboxysome shell protein CsoS1A


Mass: 9973.478 Da / Num. of mol.: 57
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 shell vertex protein CsoS4A


Mass: 8900.287 Da / Num. of mol.: 6
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
#3: Protein
Carboxysome assembly protein CsoS2B / Carboxysome assembly protein CsoS2-C


Mass: 29358.428 Da / Num. of mol.: 8
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
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: cryo-EM structure of carboxysomal midi-shell: assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T = 9 Q=12)
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

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3655 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00347609
ELECTRON MICROSCOPYf_angle_d0.47664525
ELECTRON MICROSCOPYf_dihedral_angle_d4.3517023
ELECTRON MICROSCOPYf_chiral_restr0.0457703
ELECTRON MICROSCOPYf_plane_restr0.0038583

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