7D6C

Crystal structure of CcmM N-terminal domain in complex with CcmN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Complex structure reveals CcmM and CcmN form a heterotrimeric adaptor in beta-carboxysome.

Sun, H.Cui, N.Han, S.J.Chen, Z.P.Xia, L.Y.Chen, Y.Jiang, Y.L.Zhou, C.Z.

(2021) Protein Sci 30: 1566-1576

  • DOI: https://doi.org/10.1002/pro.4090
  • Primary Citation of Related Structures:  
    7D6C

  • PubMed Abstract: 

    Carboxysome is an icosahedral self-assembled microcompartment that sequesters RuBisCO and carbonic anhydrases within a selectively permeable protein shell. The scaffolding proteins, CcmM, and CcmN were proposed to act as adaptors that crosslink the enzymatic core to shell facets. However, the details of interaction pattern remain unknown. Here we obtained a stable heterotrimeric complex of CcmM γ-carbonic anhydrase domain (termed CcmM NT ) and CcmN, with a 1:2 stoichiometry, which interacts with the shell proteins CcmO and CcmL in vitro. The 2.9 Å crystal structure of this heterotrimer revealed an asymmetric bundle composed of one CcmM NT and two CcmN subunits, all of which adopt a triangular left-handed β-helical barrel structure. The central CcmN subunit packs against CcmM NT and another CcmN subunit via a wall-to-edge or wall-to-wall pattern, respectively. Together with previous findings, we propose CcmM NT -CcmN functions as an adaptor to facilitate the recruitment of shell proteins and the assembly of intact β-carboxysome.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon dioxide concentrating mechanism protein CcmMA [auth 1],
B [auth 2]
218Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: ccmMSynpcc7942_1423
UniProt
Find proteins for Q03513 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q03513 
Go to UniProtKB:  Q03513
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03513
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome assembly protein CcmNC [auth 3],
D [auth 4],
E [auth 5],
F
122Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: ccmNSynpcc7942_1424
UniProt
Find proteins for P46204 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore P46204 
Go to UniProtKB:  P46204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46204
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.18α = 90
b = 92.33β = 90
c = 125.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31630001 and 31621002
Chinese Academy of SciencesChinaXDB37020301 and XDA24020302

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description