1OCC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 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


  • 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 hem ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
A, N
514Bos taurusGene Names: MT-CO1 (COI, COXI, MTCO1)
EC: 1.9.3.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00396 (Bos taurus)
Go to Gene View: MT-CO1
Go to UniProtKB:  P00396
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
B, O
227Bos taurusGene Names: MT-CO2 (COII, COX2, COXII, MTCO2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P68530 (Bos taurus)
Go to Gene View: MT-CO2
Go to UniProtKB:  P68530
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
C, P
261Bos taurusGene Names: MT-CO3 (COIII, COXIII, MTCO3)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00415 (Bos taurus)
Go to Gene View: MT-CO3
Go to UniProtKB:  P00415
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
D, Q
147Bos taurusGene Names: COX4I1 (COX4)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00423 (Bos taurus)
Go to Gene View: COX4I1
Go to UniProtKB:  P00423
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
E, R
109Bos taurusGene Names: COX5A
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00426 (Bos taurus)
Go to Gene View: COX5A
Go to UniProtKB:  P00426
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
F, S
98Bos taurusGene Names: COX5B
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00428 (Bos taurus)
Go to Gene View: COX5B
Go to UniProtKB:  P00428
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
G, T
84Bos taurusGene Names: COX6A2 (COX6A)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P07471 (Bos taurus)
Go to Gene View: COX6A2
Go to UniProtKB:  P07471
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
H, U
85Bos taurusGene Names: COX6B1 (COX6B)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00429 (Bos taurus)
Go to Gene View: COX6B1
Go to UniProtKB:  P00429
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
I, V
73Bos taurusGene Names: COX6C
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P04038 (Bos taurus)
Go to Gene View: COX6C
Go to UniProtKB:  P04038
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
J, W
59Bos taurusGene Names: COX7A1 (COX7A, COX7AH)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P07470 (Bos taurus)
Go to Gene View: COX7A1
Go to UniProtKB:  P07470
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
K, X
56Bos taurusGene Names: COX7B
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P13183 (Bos taurus)
Go to Gene View: COX7B
Go to UniProtKB:  P13183
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
L, Y
47Bos taurusGene Names: COX7C (COX7CP1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P00430 (Bos taurus)
Go to Gene View: COX7C
Go to UniProtKB:  P00430
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
M, Z
46Bos taurusGene Names: COX8B (COX8H)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, aa3
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download SDF File 
Download CCD File 
A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, N, O
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 189.100α = 90.00
b = 210.500β = 90.00
c = 178.600γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORrefinement
SCALEPACKdata scaling
TSUKIdata reduction
TSUKIdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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