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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
A, N
514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P00396 (Bos taurus)
Go to UniProtKB:  P00396

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
B, O
227Bos 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)
Go to UniProtKB:  P68530

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
C, P
261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P00415 (Bos taurus)
Go to UniProtKB:  P00415

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
D, Q
147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
Find proteins for P00423 (Bos taurus)
Go to UniProtKB:  P00423

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Find proteins for P00426 (Bos taurus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
F, S
98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
Find proteins for P00428 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
G, T
84Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
Find proteins for P07471 (Bos taurus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
H, U
85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
I, V
73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
Find proteins for P04038 (Bos taurus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
Find proteins for P07470 (Bos taurus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
K, X
56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
Find proteins for P13183 (Bos taurus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
L, Y
47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
Find proteins for P00430 (Bos taurus)
Go to UniProtKB:  P00430

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
M, Z
46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
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 CCD File 
A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
ZN
Query on ZN

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

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A, B, N, O
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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