8WPZ

Cryo-ET structure of RuBisCO at 3.9 angstroms from Synechococcus elongatus PCC 7942


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus beta-carboxysome.

Kong, W.W.Zhu, Y.Zhao, H.R.Du, K.Zhou, R.Q.Li, B.Yang, F.Hou, P.Huang, X.H.Chen, Y.Wang, Y.C.Sun, F.Jiang, Y.L.Zhou, C.Z.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.05.007
  • Primary Citation of Related Structures:  
    8WPZ

  • PubMed Abstract: 

    Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO 2 -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.


  • Organizational Affiliation

    School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small subunit
A, B, E, F, I
A, B, E, F, I, L, M, P
111Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31NB2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31NB2 
Go to UniProtKB:  Q31NB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31NB2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain
C, D, G, H, J
C, D, G, H, J, K, N, O
472Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for Q31NB3 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31NB3 
Go to UniProtKB:  Q31NB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31NB3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32241025

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references