1OCR

BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.

Yoshikawa, S.Shinzawa-Itoh, K.Nakashima, R.Yaono, R.Yamashita, E.Inoue, N.Yao, M.Fei, M.J.Libeu, C.P.Mizushima, T.Yamaguchi, H.Tomizaki, T.Tsukihara, T.

(1998) Science 280: 1723-1729

  • DOI: 10.1126/science.280.5370.1723
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from ...

    Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from the O2 reduction site exchanges its effective accessibility to the matrix aqueous phase for one to the cytosolic phase concomitantly with a significant decrease in the pK of its carboxyl group, on reduction of the metal sites. The movement indicates the aspartate as the proton pumping site. A tyrosine acidified by a covalently linked imidazole nitrogen is a possible proton donor for the O2 reduction by the enzyme.


    Related Citations: 
    • 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
    • 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

    Department of Life Science, Himeji Institute of Technology and CREST, Japan Science and Technology Corporation (JST), Kamigohri Akoh, Hyogo 678-1297, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEA, N514Bos 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)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEB, O227Bos 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 LengthOrganismDetails
CYTOCHROME C OXIDASEC, P261Bos 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 LengthOrganismDetails
CYTOCHROME C OXIDASED, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEE, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEF, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEH, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEI, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEJ, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEK, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEL, Y47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEM, Z46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
Find proteins for P10175 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASEG, T84Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
Find proteins for P07471 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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

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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

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A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • 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

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Entry History 

Deposition Data

  • Deposited Date: 1998-07-07 
  • Released Date: 1999-07-29 
  • Deposition Author(s): Tsukihara, T., Yao, M.

Revision History 

  • Version 1.0: 1999-07-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance