3NWV

Human cytochrome c G41S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Proapoptotic G41S Mutation to Human Cytochrome c Alters the Heme Electronic Structure and Increases the Electron Self-Exchange Rate.

Liptak, M.D.Fagerlund, R.D.Ledgerwood, E.C.Wilbanks, S.M.Bren, K.L.

(2011) J.Am.Chem.Soc. 133: 1153-1155

  • DOI: 10.1021/ja106328k

  • PubMed Abstract: 
  • The naturally occurring G41S mutation to human (Hs) cytochrome (cyt) c enhances apoptotic activity based upon previous in vitro and in vivo studies, but the molecular mechanism underlying this enhancement remains unknown. Here, X-ray crystallography, ...

    The naturally occurring G41S mutation to human (Hs) cytochrome (cyt) c enhances apoptotic activity based upon previous in vitro and in vivo studies, but the molecular mechanism underlying this enhancement remains unknown. Here, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and density functional theory (DFT) calculations have been used to identify the structural and electronic differences between wild-type (WT) and G41S Hs cyt c. S41 is part of the hydrogen bonding network for propionate 7 of heme pyrrole ring A in the X-ray structure of G41S Hs cyt c and, compared to WT, G41S Hs cyt c has increased spin density on pyrrole ring C and a faster electron self-exchange rate. DFT calculations illustrate an electronic mechanism where structural changes near ring A can result in electronic changes at ring C. Since ring C is part of the solvent-exposed protein surface, we propose that this heme electronic structure change may ultimately be responsible for the enhanced proapoptotic activity of G41S Hs cyt c.


    Related Citations: 
    • A mutation of human cytochrome c enhances the intrinsic apoptotic pathway but causes only thrombocytopenia.
      Morison, I.M.,Cramer Borde, E.M.,Cheesman, E.J.,Cheong, P.L.,Holyoake, A.J.,Fichelson, S.,Weeks, R.J.,Lo, A.,Davies, S.M.,Wilbanks, S.M.,Fagerlund, R.D.,Ludgate, M.W.,da Silva Tatley, F.M.,Coker, M.S.,Bockett, N.A.,Hughes, G.,Pippig, D.A.,Smith, M.P.,Capron, C.,Ledgerwood, E.C.
      (2008) Nat.Genet. 40: 387


    Organizational Affiliation

    Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c
A, B, C, D
104Homo sapiensMutation(s): 1 
Gene Names: CYCS (CYC)
Find proteins for P99999 (Homo sapiens)
Go to Gene View: CYCS
Go to UniProtKB:  P99999
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.632α = 90.00
b = 62.693β = 89.78
c = 35.470γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CrystalCleardata collection
REFMACrefinement
d*TREKdata scaling
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance