Structure of recombinant human cytochrome c

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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The Hydrogen Peroxide Induced Radical Behaviour in Human Cytochrome C Phospholipid Complexes: Implications for the Enhanced Pro-Apoptotic Activity of the G41S Mutant

Rajagopal, B.S.Edzuma, A.N.Hough, M.A.Blundell, K.L.I.M.Kagan, V.E.Kapralov, A.A.Fraser, L.A.Butt, J.N.Silkstone, G.G.Wilson, M.T.Svistunenko, D.A.Worrall, J.A.R.

(2013) Biochem J 456: 441

  • DOI: https://doi.org/10.1042/BJ20130758
  • Primary Citation of Related Structures:  
    3ZCF, 3ZOO

  • PubMed Abstract: 

    We have investigated whether the pro-apoptotic properties of the G41S mutant of human cytochrome c can be explained by a higher than wild-type peroxidase activity triggered by phospholipid binding. A key complex in mitochondrial apoptosis involves cytochrome c and the phospholipid cardiolipin. In this complex cytochrome c has its native axial Met(80) ligand dissociated from the haem-iron, considerably augmenting the peroxidase capability of the haem group upon H2O2 binding. By EPR spectroscopy we reveal that the magnitude of changes in the paramagnetic haem states, as well as the yield of protein-bound free radical, is dependent on the phospholipid used and is considerably greater in the G41S mutant. A high-resolution X-ray crystal structure of human cytochrome c was determined and, in combination with the radical EPR signal analysis, two tyrosine residues, Tyr(46) and Tyr(48), have been rationalized to be putative radical sites. Subsequent single and double tyrosine-to-phenylalanine mutations revealed that the EPR signal of the radical, found to be similar in all variants, including G41S and wild-type, originates not from a single tyrosine residue, but is instead a superimposition of multiple EPR signals from different radical sites. We propose a mechanism of multiple radical formations in the cytochrome c-phospholipid complexes under H2O2 treatment, consistent with the stabilization of the radical in the G41S mutant, which elicits a greater peroxidase activity from cytochrome c and thus has implications in mitochondrial apoptosis.

  • Organizational Affiliation

    *School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
104Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P99999 (Homo sapiens)
Explore P99999 
Go to UniProtKB:  P99999
GTEx:  ENSG00000172115 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP99999
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.545α = 76.54
b = 53.915β = 88.57
c = 58.723γ = 72.1
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description