2GB8

Solution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c peroxidase


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR.

Volkov, A.N.Worrall, J.A.Holtzmann, E.Ubbink, M.

(2006) Proc.Natl.Acad.Sci.Usa 103: 18945-18950

  • DOI: 10.1073/pnas.0603551103

  • PubMed Abstract: 
  • The physiological complex of yeast cytochrome c peroxidase and iso-1-cytochrome c is a paradigm for biological electron transfer. Using paramagnetic NMR spectroscopy, we have determined the conformation of the protein complex in solution, which is sh ...

    The physiological complex of yeast cytochrome c peroxidase and iso-1-cytochrome c is a paradigm for biological electron transfer. Using paramagnetic NMR spectroscopy, we have determined the conformation of the protein complex in solution, which is shown to be very similar to that observed in the crystal structure [Pelletier H, Kraut J (1992) Science 258:1748-1755]. Our results support the view that this transient electron transfer complex is dynamic. The solution structure represents the dominant protein-protein orientation, which, according to our estimates, is occupied for >70% of the lifetime of the complex, with the rest of the time spent in the dynamic encounter state. Based on the observed paramagnetic effects, we have delineated the conformational space sampled by the protein molecules during the dynamic part of the interaction, providing experimental support for the theoretical predictions of the classical Brownian dynamics study [Northrup SH, Boles JO, Reynolds JCL (1988) Science 241:67-70]. Our findings corroborate the dynamic behavior of this complex and offer an insight into the mechanism of the protein complex formation in solution.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c peroxidase
A
294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CCP1 (CCP, CPO)
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c iso-1
B
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2GB8 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance