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- PDB-8wpz: Cryo-ET structure of RuBisCO at 3.9 angstroms from Synechococcus ... -

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Basic information

Entry
Database: PDB / ID: 8wpz
TitleCryo-ET structure of RuBisCO at 3.9 angstroms from Synechococcus elongatus PCC 7942
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunitRuBisCO
KeywordsPHOTOSYNTHESIS / carboxysome / RuBisCO / cryo-et
Function / homology
Function and homology information


carboxysome / photorespiration / 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 / subtomogram averaging / cryo EM / Resolution: 3.9 Å
AuthorsKong, W.W. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241025 China
CitationJournal: To Be Published
Title: Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus beta-carboxysome
Authors: Kong, W.W. / Zhu, Y. / Zhao, H.R. / Du, K. / Zhou, R.Q. / Li, B. / Yang, F. / Hou, P. / Chen, Y. / Sun, F. / Jiang, Y.L. / Zhou, C.Z.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase small subunit
B: Ribulose bisphosphate carboxylase small subunit
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small subunit
F: Ribulose bisphosphate carboxylase small subunit
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase small subunit
J: Ribulose bisphosphate carboxylase large chain
K: Ribulose bisphosphate carboxylase large chain
L: Ribulose bisphosphate carboxylase small subunit
M: Ribulose bisphosphate carboxylase small subunit
N: Ribulose bisphosphate carboxylase large chain
O: Ribulose bisphosphate carboxylase large chain
P: Ribulose bisphosphate carboxylase small subunit


Theoretical massNumber of molelcules
Total (without water)526,92616
Polymers526,92616
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ribulose bisphosphate carboxylase small subunit / RuBisCO / RuBisCO small subunit


Mass: 13349.196 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31NB2
#2: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52516.605 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

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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: RuBisCO / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Nostoc sp. PCC 7120 = FACHB-418
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K

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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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 145 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2700 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 88 / Num. of volumes extracted: 29000
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0136718
ELECTRON MICROSCOPYf_angle_d0.94249732
ELECTRON MICROSCOPYf_dihedral_angle_d4.7734900
ELECTRON MICROSCOPYf_chiral_restr0.0445236
ELECTRON MICROSCOPYf_plane_restr0.0066506

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