1OCC

STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.

Tsukihara, T.Aoyama, H.Yamashita, E.Tomizaki, T.Yamaguchi, H.Shinzawa-Itoh, K.Nakashima, R.Yaono, R.Yoshikawa, S.

(1996) Science 272: 1136-1144

  • DOI: 10.1126/science.272.5265.1136
  • Primary Citation of Related Structures:  
    1OCC

  • PubMed Abstract: 
  • The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A ...

    The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water molecules, and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified.


    Related Citations: 
    • Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase at 2.8 A
      Tsukihara, T., Aoyama, H., Yamashita, E., Tomizaki, T., Yamaguchi, H., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yoshikawa, S.
      (1995) Science 269: 1069

    Organizational Affiliation

    Institute for Protein Research, Osaka University, Suita, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE AN514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE BO227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P68530 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE CP261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE DQ147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE ER109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Find proteins for P00426 (Bos taurus)
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Entity ID: 6
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CYTOCHROME C OXIDASE FS98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE GT84Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE HU85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE IV73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE JW59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
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Entity ID: 11
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CYTOCHROME C OXIDASE KX56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
Find proteins for P13183 (Bos taurus)
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Entity ID: 12
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CYTOCHROME C OXIDASE LY47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE MZ46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
Find proteins for P10175 (Bos taurus)
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.1α = 90
b = 210.5β = 90
c = 178.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TSUKIdata reduction
X-PLORmodel building
X-PLORrefinement
TSUKIdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-21
    Changes: Data collection