2N3Y | pdb_00002n3y

NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 2N3Y

This is version 1.2 of the entry. See complete history

Literature

Structural basis of mitochondrial dysfunction in response to cytochrome c phosphorylation at tyrosine 48.

Moreno-Beltran, B.Guerra-Castellano, A.Diaz-Quintana, A.Del Conte, R.Garcia-Maurino, S.M.Diaz-Moreno, S.Gonzalez-Arzola, K.Santos-Ocana, C.Velazquez-Campoy, A.De la Rosa, M.A.Turano, P.Diaz-Moreno, I.

(2017) Proc Natl Acad Sci U S A 114: E3041-E3050

  • DOI: https://doi.org/10.1073/pnas.1618008114
  • Primary Citation Related Structures: 
    2N3Y

  • PubMed Abstract: 

    Regulation of mitochondrial activity allows cells to adapt to changing conditions and to control oxidative stress, and its dysfunction can lead to hypoxia-dependent pathologies such as ischemia and cancer. Although cytochrome c phosphorylation-in particular, at tyrosine 48-is a key modulator of mitochondrial signaling, its action and molecular basis remain unknown. Here we mimic phosphorylation of cytochrome c by replacing tyrosine 48 with p -carboxy-methyl-l-phenylalanine ( p CMF). The NMR structure of the resulting mutant reveals significant conformational shifts and enhanced dynamics around p CMF that could explain changes observed in its functionality: The phosphomimetic mutation impairs cytochrome c diffusion between respiratory complexes, enhances hemeprotein peroxidase and reactive oxygen species scavenging activities, and hinders caspase-dependent apoptosis. Our findings provide a framework to further investigate the modulation of mitochondrial activity by phosphorylated cytochrome c and to develop novel therapeutic approaches based on its prosurvival effects.


  • Organizational Affiliation
    • Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla-Spanish National Scientific Council (CSIC), 41092 Seville, Spain.

Macromolecule Content 

  • Total Structure Weight: 12.3 kDa 
  • Atom Count: 862 
  • Modeled Residue Count: 104 
  • Deposited Residue Count: 104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c104Homo sapiensMutation(s): 1 
Gene Names: CYCSCYC
UniProt & NIH Common Fund Data Resources
Find proteins for P99999 (Homo sapiens)
Explore P99999 
Go to UniProtKB:  P99999
PHAROS:  P99999
GTEx:  ENSG00000172115 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP99999
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MH0

Query on MH0



Download:Ideal Coordinates CCD File
B [auth A]Mesoheme
C34 H36 Fe N4 O4
CKMCSMAXNUVLQI-RGGAHWMASA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
1PA
Query on 1PA
A
L-PEPTIDE LINKINGC11 H13 N O4PHE

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary