1V54

Bovine heart cytochrome c oxidase at the fully oxidized state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.

Tsukihara, T., Shimokata, K., Katayama, Y., Shimada, H., Muramoto, K., Aoyama, H., Mochizuki, M., Shinzawa-Itoh, K., Yamashita, E., Yao, M., Ishimura, Y., Yoshikawa, S.

(2003) Proc Natl Acad Sci U S A 100: 15304-15309

  • DOI: 10.1073/pnas.2635097100
  • Primary Citation of Related Structures:  
    1V55, 1V54

  • PubMed Abstract: 

    • Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near th ...

    Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near the enzyme surface, undergoes a redox-coupled x-ray structural change, which is suggestive of a role for this residue in redox-driven proton pumping. However, functional or mechanistic evidence for the involvement of this residue in proton pumping has not yet been obtained. We report that the Asp-51 --> Asn mutation of the bovine enzyme abolishes its proton-pumping function without impairment of the dioxygen reduction activity. Improved x-ray structures (at 1.8/1.9-A resolution in the fully oxidized/reduced states) show that the net positive charge created upon oxidation of the low-spin heme of the enzyme drives the active proton transport from the interior of the mitochondria to Asp-51 across the enzyme via a water channel and a hydrogen-bond network, located in tandem, and that the enzyme reduction induces proton ejection from the aspartate to the mitochondrial exterior. A peptide bond in the hydrogen-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of the low-spin heme, suggests that the channel functions as an effective proton-collecting region. Infrared results indicate that the conformation of Asp-51 is controlled only by the oxidation state of the low-spin heme. These results indicate that the low-spin heme drives the proton-pumping process.

    Organizational Affiliation: 

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide I A, N514Bos taurusMutation(s): 0 
Gene Names: MT-CO1, COI, COXI, MTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P00396 (Bos taurus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide II B, O227Bos taurusMutation(s): 0 
Gene Names: MT-CO2, COII, COX2, COXII, MTCO2
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P68530 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide III C, P261Bos taurusMutation(s): 0 
Gene Names: MT-CO3, COIII, COXIII, MTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P00415 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit IV isoform 1 D, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1, COX4
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P00423 (Bos taurus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide Va E, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide Vb F, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P00428 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIa-heart G, T85Bos taurusMutation(s): 0 
Gene Names: COX6A2, COX6A
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P07471 (Bos taurus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIb H, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1, COX6B
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIc I, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P04038 (Bos taurus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIa-heart J, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1, COX7A, COX7AH
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P07470 (Bos taurus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIb K, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P13183 (Bos taurus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIc L, Y47Bos taurusMutation(s): 0 
Gene Names: COX7C, COX7CP1
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII-heart M, Z46Bos taurusMutation(s): 0 
Gene Names: COX8B, COX8H
EC: 1.9.3.1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Fully Oxidized Cytochrome C Oxidase, aa3
Find proteins for P10175 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
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C, G, P, T
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L		 Ligand Interaction
TGL
Query on TGL
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A, D, L, N, Q
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N		 Ligand Interaction
HEA
Query on HEA
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A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L		 Ligand Interaction
PEK
Query on PEK
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C, G, P, T
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N		 Ligand Interaction
PSC
Query on PSC
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E, O
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O		 Ligand Interaction
PGV
Query on PGV
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A, C, N, P
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N		 Ligand Interaction
DMU
Query on DMU
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M, Z
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N		 Ligand Interaction
CHD
Query on CHD
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B, C, J, O, P, W
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N		 Ligand Interaction
CUA
Query on CUA
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B, O
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N		 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, N
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
UNX
Query on UNX
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C, P
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME		A,NL-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO		G,TL-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC		I,VL-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.59α = 90
b = 205.14β = 90
c = 178.25γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance