9IUR | pdb_00009iur

Crystal structure of CcmS from Synechocystis sp. PCC 6803

  • Classification: CHAPERONE
  • Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2024-07-22 Released: 2025-03-12 
  • Deposition Author(s): Li, J., Deng, J.X., Jiang, Y.L., Zhou, C.Z.
  • Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), Anhui Provincial Key Research and Development Project, Chaohu Lake Biological Resource Investigation and Research Project, USTC Research Funds of the Double First-Class Initiative, Youth Innovation Promotion Association of the Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.272 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Assembly mechanism of the beta-carboxysome shell mediated by the chaperone CcmS.

Li, J.Deng, J.X.Chen, X.Li, B.Li, B.R.Zhu, Z.L.Liu, J.Chen, Y.Mi, H.Zhou, C.Z.Jiang, Y.L.

(2025) New Phytol 246: 1676-1690

  • DOI: https://doi.org/10.1111/nph.70086
  • Primary Citation of Related Structures:  
    9IUR, 9IV3, 9IV7

  • PubMed Abstract: 

    Carboxysomes are self-assembled bacterial microcompartments (BMCs) that encapsulate the enzymes RuBisCO and carbonic anhydrase into a proteinaceous shell, enhancing the efficiency of photosynthetic carbon fixation. The chaperone CcmS was reported to participate in the assembly of β-carboxysomes; however, the underlying molecular mechanism remains elusive. We report the crystal structure of CcmS from Synechocystis sp. PCC 6803, revealing a monomer of α/β fold. Moreover, its complex structures with two types of BMC hexamers, CcmK1 homohexamer and CcmK1-CcmK2 heterohexamer, reveal a same pattern of CcmS binding to the featured C-terminal segment of CcmK1. Upon binding to CcmS, this C-terminal segment of CcmK1 is folded into an amphipathic α-helix protruding outward that might function as a hinge to crosslink adjacent BMC-H hexamers, thereby facilitating concerted and precise assembly of the β-carboxysome shell. Deletion of the ccmS gene or the 8-residue C-terminal coding region of ccmK1 resulted in the formation of aberrant and fewer carboxysomes, suppressed photosynthetic capacity in Synechocystis sp. PCC 6803. These findings enable us to propose a putative model for the chaperone-assisted assembly of β-carboxysome shell and provide clues for the design and engineering of efficient carbon fixation machinery.


  • Organizational Affiliation
    • School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Slr1911 protein
A, B, C, D, E
136Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: slr1911
UniProt
Find proteins for P73106 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P73106 
Go to UniProtKB:  P73106
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73106
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth E],
T [auth E],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Y [auth E]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.963α = 90
b = 132.963β = 90
c = 38.085γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDA24020302
National Natural Science Foundation of China (NSFC)China32171198
National Natural Science Foundation of China (NSFC)China32241025
Anhui Provincial Key Research and Development ProjectChina2022l07020034
Chaohu Lake Biological Resource Investigation and Research ProjectChina2020-340181-77-01-037328
USTC Research Funds of the Double First-Class InitiativeChinaYD9100002023
Youth Innovation Promotion Association of the Chinese Academy of SciencesChina2020452

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references