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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 subunit
KeywordsPHOTOSYNTHESIS / carboxysome / RuBisCO / cryo-et
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 / 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: Structure / Year: 2024
Title: Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus β-carboxysome.
Authors: Wen-Wen Kong / Yun Zhu / Heng-Rui Zhao / Kang Du / Rui-Qian Zhou / Bo Li / Feng Yang / Pu Hou / Xia-He Huang / Yuxing Chen / Ying-Chun Wang / Fei Sun / Yong-Liang Jiang / Cong-Zhao Zhou /
Abstract: Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of ...Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of thousands of individual proteins; however, the packaging pattern of internal RuBisCOs remains largely unknown. Here we purified the intact β-carboxysomes from Synechococcus elongatus PCC 7942 and identified the protein components by mass spectrometry. Cryo-electron tomography combined with subtomogram averaging revealed the general organization pattern of internal RuBisCOs, in which the adjacent RuBisCOs are mainly arranged in three distinct manners: head-to-head, head-to-side, and side-by-side. The RuBisCOs in the outermost layer are regularly aligned along the shell, the majority of which directly interact with the shell. Moreover, statistical analysis enabled us to propose an ideal packaging model of RuBisCOs in the β-carboxysome. These results provide new insights into the biogenesis of β-carboxysomes and also advance our understanding of the efficient carbon fixation functionality of carboxysomes.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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 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
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: 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 FIELD / 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 software
IDNameVersionCategory
8PHENIXmodel refinement
13RELION3.13D 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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