6N1O | pdb_00006n1o

Oxidized rat cytochrome c mutant (S47E)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Serine-47 phosphorylation of cytochromecin the mammalian brain regulates cytochromecoxidase and caspase-3 activity.

Kalpage, H.A.Vaishnav, A.Liu, J.Varughese, A.Wan, J.Turner, A.A.Ji, Q.Zurek, M.P.Kapralov, A.A.Kagan, V.E.Brunzelle, J.S.Recanati, M.A.Grossman, L.I.Sanderson, T.H.Lee, I.Salomon, A.R.Edwards, B.F.P.Huttemann, M.

(2019) FASEB J 33: 13503-13514

  • DOI: https://doi.org/10.1096/fj.201901120R
  • Primary Citation of Related Structures:  
    5C0Z, 6N1O

  • PubMed Abstract: 

    Cytochrome c (Cyt c ) is a multifunctional protein that operates as an electron carrier in the mitochondrial electron transport chain and plays a key role in apoptosis. We have previously shown that tissue-specific phosphorylations of Cyt c in the heart, liver, and kidney play an important role in the regulation of cellular respiration and cell death. Here, we report that Cyt c purified from mammalian brain is phosphorylated on S47 and that this phosphorylation is lost during ischemia. We have characterized the functional effects in vitro using phosphorylated Cyt c purified from pig brain tissue and a recombinant phosphomimetic mutant (S47E). We crystallized S47E phosphomimetic Cyt c at 1.55 Å and suggest that it spatially matches S47-phosphorylated Cyt c , making it a good model system. Both S47-phosphorylated and phosphomimetic Cyt c showed a lower oxygen consumption rate in reaction with isolated Cyt c oxidase, which we propose maintains intermediate mitochondrial membrane potentials under physiologic conditions, thus minimizing production of reactive oxygen species. S47-phosphorylated and phosphomimetic Cyt c showed lower caspase-3 activity. Furthermore, phosphomimetic Cyt c had decreased cardiolipin peroxidase activity and is more stable in the presence of H 2 O 2 . Our data suggest that S47 phosphorylation of Cyt c is tissue protective and promotes cell survival in the brain.-Kalpage, H. A., Vaishnav, A., Liu, J., Varughese, A., Wan, J., Turner, A. A., Ji, Q., Zurek, M. P., Kapralov, A. A., Kagan, V. E., Brunzelle, J. S., Recanati, M.-A., Grossman, L. I., Sanderson, T. H., Lee, I., Salomon, A. R., Edwards, B. F. P, Hüttemann, M. Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity.


  • Organizational Affiliation

    Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c, somatic
A, B, C, D
104Rattus norvegicusMutation(s): 1 
Gene Names: Cycs
UniProt
Find proteins for P62898 (Rattus norvegicus)
Explore P62898 
Go to UniProtKB:  P62898
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62898
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
N [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
FC6
Query on FC6

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
K [auth B],
M [auth C]
HEXACYANOFERRATE(3-)
C6 Fe N6
HCMVSLMENOCDCK-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.705α = 109.89
b = 52.357β = 92.66
c = 61.819γ = 91.15
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

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 Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM1166807

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary