RCSB PDB - 9KRR: CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM Synechocystis PCC 6803

 9KRR

CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM Synechocystis PCC 6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.210 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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Literature

A High-Resolution Crystallographic Study of Cytochrome c6: Structural Basis for Electron Transfer in Cyanobacterial Photosynthesis.

Zhang, B.Xu, Y.Liu, S.Chen, S.Zhao, W.Li, Z.Wang, J.Zhao, W.Zhang, H.Dong, Y.Gong, Y.Sheng, W.Cao, P.

(2025) Int J Mol Sci 26

  • DOI: https://doi.org/10.3390/ijms26020824
  • Primary Citation of Related Structures:  
    9KRC, 9KRD, 9KRR

  • PubMed Abstract: 

    Cyanobacterial cytochrome c6 (Cyt c6) is crucial for electron transfer between the cytochrome b6f complex and photosystem I (PSI), playing a key role in photosynthesis and enhancing adaptation to extreme environments. This study investigates the high-resolution crystal structures of Cyt c6 from Synechococcus elongatus PCC 7942 and Synechocystis PCC 6803, focusing on its dimerization mechanisms and functional implications for photosynthesis. Cyt c6 was expressed in Escherichia coli using a dual-plasmid co-expression system and characterized in both oxidized and reduced states. X-ray crystallography revealed three distinct crystal forms, with asymmetric units containing 2, 4, or 12 molecules, all of which consist of repeating dimeric structures. Structural comparisons across species indicated that dimerization predominantly occurs through hydrophobic interactions within a conserved motif around the heme crevice, despite notable variations in dimer positioning. We propose that the dimerization of Cyt c6 enhances structural stability, optimizes electron transfer kinetics, and protects the protein from oxidative damage. Furthermore, we used AlphaFold3 to predict the structure of the PSI-Cyt c6 complex, revealing specific interactions that may facilitate efficient electron transfer. These findings provide new insights into the functional role of Cyt c6 dimerization and its contribution to improving cyanobacterial photosynthetic electron transport.


  • Organizational Affiliation

    College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c6
A, B, C, D, E
87Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: petJsll1796
UniProt
Find proteins for P46445 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P46445 
Go to UniProtKB:  P46445
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46445
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
BA [auth D]
CB [auth J]
FA [auth E]
GB [auth K]
KA [auth F]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth I]
BB [auth I]
EA [auth D]
FB [auth J]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
DB [auth J]
EB [auth J]
GA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.210 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.899α = 90
b = 74.437β = 106.111
c = 133.182γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070259

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references