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- PDB-8bcm: Structure of Synechococcus elongatus PCC 7942 Rubisco recombinant... -

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Basic information

Entry
Database: PDB / ID: 8bcm
TitleStructure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli
Components
  • Ribulose 1,5-bisphosphate carboxylase small subunit
  • Ribulose bisphosphate carboxylase large chain
KeywordsBIOSYNTHETIC PROTEIN / Rubisco / Synechococcus / carbon dioxide fixation / recombinant expression
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
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, 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
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsNi, T. / Sun, Y. / Liu, L.N. / Zhang, P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Structure of Rubisco
Authors: Sun, Y. / Ni, T.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
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Revision 1.0Nov 1, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 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
D: Ribulose 1,5-bisphosphate carboxylase small subunit
C: Ribulose bisphosphate carboxylase large chain
E: Ribulose 1,5-bisphosphate carboxylase small subunit
K: Ribulose 1,5-bisphosphate carboxylase small subunit
N: Ribulose 1,5-bisphosphate carboxylase small subunit
L: Ribulose 1,5-bisphosphate carboxylase small subunit
O: Ribulose 1,5-bisphosphate carboxylase small subunit
M: Ribulose 1,5-bisphosphate carboxylase small subunit
P: Ribulose 1,5-bisphosphate carboxylase small subunit
B: Ribulose bisphosphate carboxylase large chain
A: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase large chain
G: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase large chain


Theoretical massNumber of molelcules
Total (without water)526,92616
Polymers526,92616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ribulose 1,5-bisphosphate carboxylase small subunit


Mass: 13349.196 Da / Num. of mol.: 8 / Fragment: Rubisco small subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_1427 / Production host: Escherichia coli (E. coli)
References: UniProt: Q31NB2, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52516.605 Da / Num. of mol.: 8 / Fragment: Rubisco large subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / Gene: cbbL, rbcL, Synpcc7942_1426 / Production host: Escherichia coli (E. coli)
References: UniProt: Q31NB3, ribulose-bisphosphate carboxylase
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: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219865 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00534352
ELECTRON MICROSCOPYf_angle_d0.65546496
ELECTRON MICROSCOPYf_dihedral_angle_d5.4414592
ELECTRON MICROSCOPYf_chiral_restr0.0464944
ELECTRON MICROSCOPYf_plane_restr0.0056096

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