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- PDB-9fwv: Rubisco in native beta-carboxysomes -

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Basic information

Entry
Database: PDB / ID: 9fwv
TitleRubisco in native beta-carboxysomes
Components
  • Carboxysome assembly protein CcmM
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit
KeywordsPHOTOSYNTHESIS / Rubisco / CcmM
Function / homology
Function and homology information


structural constituent of carboxysome shell / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / monooxygenase activity / magnesium ion binding
Similarity search - Function
Carboxysome assembly protein CcmM / : / : / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site ...Carboxysome assembly protein CcmM / : / : / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase small subunit / Carboxysome assembly protein CcmM / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3.5 Å
AuthorsSheng, Y. / Hardenbrook, N. / Li, K.
Funding support United Kingdom, European Union, China, 9items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V009729/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003339/1 United Kingdom
Royal SocietyURFR180030 United Kingdom
Royal SocietyRGFEA181061 United Kingdom
Leverhulme TrustRPG-2021-286 United Kingdom
Leverhulme TrustRPG-2019-300 United Kingdom
European Research Council (ERC)101021133European Union
Wellcome Trust206422/Z/17/Z United Kingdom
National Natural Science Foundation of China (NSFC)32070109 China
CitationJournal: Plant Physiol / Year: 2024
Title: Rubisco packaging and stoichiometric composition of the native β-carboxysome in Synechococcus elongatus PCC7942.
Authors: Yaqi Sun / Yuewen Sheng / Tao Ni / Xingwu Ge / Joscelyn Sarsby / Philip J Brownridge / Kang Li / Nathan Hardenbrook / Gregory F Dykes / Nichola Rockliffe / Claire E Eyers / Peijun Zhang / Lu-Ning Liu /
Abstract: Carboxysomes are anabolic bacterial microcompartments that play an essential role in CO2 fixation in cyanobacteria. This self-assembling proteinaceous organelle uses a polyhedral shell constructed by ...Carboxysomes are anabolic bacterial microcompartments that play an essential role in CO2 fixation in cyanobacteria. This self-assembling proteinaceous organelle uses a polyhedral shell constructed by hundreds of shell protein paralogs to encapsulate the key CO2-fixing enzymes Rubisco and carbonic anhydrase. Deciphering the precise arrangement and structural organization of Rubisco enzymes within carboxysomes is crucial for understanding carboxysome formation and overall functionality. Here, we employed cryoelectron tomography and subtomogram averaging to delineate the 3D packaging of Rubiscos within β-carboxysomes in the freshwater cyanobacterium Synechococcus elongatus PCC7942 grown under low light. Our results revealed that Rubiscos are arranged in multiple concentric layers parallel to the shell within the β-carboxysome lumen. We also detected Rubisco binding with the scaffolding protein CcmM in β-carboxysomes, which is instrumental for Rubisco encapsulation and β-carboxysome assembly. Using Quantification conCATamer-based quantitative MS, we determined the absolute stoichiometric composition of the entire β-carboxysome. This study provides insights into the assembly principles and structural variation of β-carboxysomes, which will aid in the rational design and repurposing of carboxysome nanostructures for diverse bioengineering applications.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxysome assembly protein CcmM
B: Carboxysome assembly protein CcmM
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase small subunit
E: Ribulose bisphosphate carboxylase small subunit
F: Carboxysome assembly protein CcmM
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase large chain
K: Ribulose bisphosphate carboxylase small subunit
L: Ribulose bisphosphate carboxylase small subunit
M: Ribulose bisphosphate carboxylase small subunit
N: Ribulose bisphosphate carboxylase small subunit
O: Ribulose bisphosphate carboxylase small subunit
P: Ribulose bisphosphate carboxylase small subunit
Q: Ribulose bisphosphate carboxylase large chain
R: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase large chain
T: Carboxysome assembly protein CcmM


Theoretical massNumber of molelcules
Total (without water)529,63520
Polymers529,63520
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Carboxysome assembly protein CcmM / CcmM58 / M58 / Carbon dioxide concentrating mechanism protein CcmM / Carboxysome shell associated protein CcmM


Mass: 9944.059 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: LSSEVITQVRSLLNQGYRIGTEHADKRRFRTSSWQPCAPIQSTNERQVLSELENCLSEHEGEYVRLLGIDTNTRSRVFEALIQRPD
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q03513
#2: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 49050.590 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31NB3, ribulose-bisphosphate carboxylase
#3: Protein
Ribulose bisphosphate carboxylase small subunit / RuBisCO small subunit


Mass: 12181.751 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: P04716
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: complex of Rubisco abd CcmM Small-subunit-like domain in lumens of purified beta-carboxysomes
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5500 nm / Nominal defocus min: 2500 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
8PHENIXmodel refinement
11emClarityfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 65 / Num. of volumes extracted: 185

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