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- PDB-8wxb: Cryo-EM structure of the alpha-carboxysome shell vertex from Proc... -

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Basic information

Entry
Database: PDB / ID: 8wxb
TitleCryo-EM structure of the alpha-carboxysome shell vertex from Prochlorococcus MED4
Components
  • Carboxysome assembly protein CsoS2
  • Carboxysome shell vertex protein CsoS4A
  • Major carboxysome shell protein CsoS1
KeywordsPHOTOSYNTHESIS / alpha-carboxysome / carbon fixation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsJiang, Y.L. / Zhou, R.Q. / Zhou, C.Z. / Zeng, Q.L.
Funding support China, Hong Kong, 5items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: Carboxysome shell vertex protein CsoS4A
A: Major carboxysome shell protein CsoS1
B: Major carboxysome shell protein CsoS1
C: Major carboxysome shell protein CsoS1
D: Major carboxysome shell protein CsoS1
E: Major carboxysome shell protein CsoS1
F: Major carboxysome shell protein CsoS1
G: Major carboxysome shell protein CsoS1
H: Major carboxysome shell protein CsoS1
I: Major carboxysome shell protein CsoS1
J: Major carboxysome shell protein CsoS1
K: Major carboxysome shell protein CsoS1
L: Major carboxysome shell protein CsoS1
M: Major carboxysome shell protein CsoS1
N: Major carboxysome shell protein CsoS1
O: Major carboxysome shell protein CsoS1
P: Major carboxysome shell protein CsoS1
Q: Major carboxysome shell protein CsoS1
R: Major carboxysome shell protein CsoS1
S: Major carboxysome shell protein CsoS1
T: Major carboxysome shell protein CsoS1
U: Major carboxysome shell protein CsoS1
V: Major carboxysome shell protein CsoS1
W: Major carboxysome shell protein CsoS1
X: Major carboxysome shell protein CsoS1
Y: Carboxysome assembly protein CsoS2
Z: Carboxysome assembly protein CsoS2
a: Major carboxysome shell protein CsoS1
b: Major carboxysome shell protein CsoS1
c: Major carboxysome shell protein CsoS1
d: Major carboxysome shell protein CsoS1
e: Major carboxysome shell protein CsoS1
f: Major carboxysome shell protein CsoS1
g: Major carboxysome shell protein CsoS1
h: Major carboxysome shell protein CsoS1
i: Major carboxysome shell protein CsoS1
j: Major carboxysome shell protein CsoS1
k: Major carboxysome shell protein CsoS1
l: Major carboxysome shell protein CsoS1
m: Major carboxysome shell protein CsoS1
n: Major carboxysome shell protein CsoS1
o: Major carboxysome shell protein CsoS1
p: Major carboxysome shell protein CsoS1
q: Major carboxysome shell protein CsoS1
r: Major carboxysome shell protein CsoS1
s: Major carboxysome shell protein CsoS1
t: Major carboxysome shell protein CsoS1
u: Major carboxysome shell protein CsoS1
v: Major carboxysome shell protein CsoS1
w: Major carboxysome shell protein CsoS1
x: Major carboxysome shell protein CsoS1


Theoretical massNumber of molelcules
Total (without water)655,84551
Polymers655,84551
Non-polymers00
Water00
1
2: Carboxysome shell vertex protein CsoS4A
A: Major carboxysome shell protein CsoS1
B: Major carboxysome shell protein CsoS1
C: Major carboxysome shell protein CsoS1
D: Major carboxysome shell protein CsoS1
E: Major carboxysome shell protein CsoS1
F: Major carboxysome shell protein CsoS1
G: Major carboxysome shell protein CsoS1
H: Major carboxysome shell protein CsoS1
I: Major carboxysome shell protein CsoS1
J: Major carboxysome shell protein CsoS1
K: Major carboxysome shell protein CsoS1
L: Major carboxysome shell protein CsoS1
M: Major carboxysome shell protein CsoS1
N: Major carboxysome shell protein CsoS1
O: Major carboxysome shell protein CsoS1
P: Major carboxysome shell protein CsoS1
Q: Major carboxysome shell protein CsoS1
R: Major carboxysome shell protein CsoS1
S: Major carboxysome shell protein CsoS1
T: Major carboxysome shell protein CsoS1
U: Major carboxysome shell protein CsoS1
V: Major carboxysome shell protein CsoS1
W: Major carboxysome shell protein CsoS1
X: Major carboxysome shell protein CsoS1
Y: Carboxysome assembly protein CsoS2
Z: Carboxysome assembly protein CsoS2
a: Major carboxysome shell protein CsoS1
b: Major carboxysome shell protein CsoS1
c: Major carboxysome shell protein CsoS1
d: Major carboxysome shell protein CsoS1
e: Major carboxysome shell protein CsoS1
f: Major carboxysome shell protein CsoS1
g: Major carboxysome shell protein CsoS1
h: Major carboxysome shell protein CsoS1
i: Major carboxysome shell protein CsoS1
j: Major carboxysome shell protein CsoS1
k: Major carboxysome shell protein CsoS1
l: Major carboxysome shell protein CsoS1
m: Major carboxysome shell protein CsoS1
n: Major carboxysome shell protein CsoS1
o: Major carboxysome shell protein CsoS1
p: Major carboxysome shell protein CsoS1
q: Major carboxysome shell protein CsoS1
r: Major carboxysome shell protein CsoS1
s: Major carboxysome shell protein CsoS1
t: Major carboxysome shell protein CsoS1
u: Major carboxysome shell protein CsoS1
v: Major carboxysome shell protein CsoS1
w: Major carboxysome shell protein CsoS1
x: Major carboxysome shell protein CsoS1
x 5


Theoretical massNumber of molelcules
Total (without water)3,279,227255
Polymers3,279,227255
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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: C5 (5 fold cyclic))

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Components

#1: Protein Carboxysome shell vertex protein CsoS4A


Mass: 9407.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus sp. MED4 (bacteria) / References: UniProt: Q7V2C6
#2: Protein ...
Major carboxysome shell protein CsoS1


Mass: 10050.501 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus sp. MED4 (bacteria) / References: UniProt: Q7V2D1
#3: Protein Carboxysome assembly protein CsoS2 / Carboxysome shell protein CsoS2


Mass: 82006.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus sp. MED4 (bacteria) / References: UniProt: Q7V2C8

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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: The shell vertex of alpha-carboxysome / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 3.4 MDa / Experimental value: NO
Source (natural)Organism: Prochlorococcus sp. MED4 (bacteria)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28093 / Symmetry type: POINT

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