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 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7COH


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

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide I
A, N
514Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide II
B, O
227Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide III
C, P
261Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit IV isoform 1
D, Q
147Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide Va
E, R
109Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide Vb
F, S
98Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIa-heart
G, T
85Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIb
H, U
85Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIc
I, V
73Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIa-heart
J, W
59Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIb
K, X
56Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIc
L, Y
47Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII-heart
M, Z
46Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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MA [auth C],
OB [auth P],
VA [auth G],
XB [auth T]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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FA [auth A]
FB [auth N]
GB [auth N]
SA [auth D]
UB [auth Q]
FA [auth A],
FB [auth N],
GB [auth N],
SA [auth D],
UB [auth Q],
YA [auth L]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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DA [auth A],
DB [auth N],
EA [auth A],
EB [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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NA [auth C]
OA [auth C]
PB [auth P]
QB [auth P]
WA [auth G]
NA [auth C],
OA [auth C],
PB [auth P],
QB [auth P],
WA [auth G],
WB [auth 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
PSC
Query on PSC

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KB [auth O],
TA [auth E]
(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
PGV
Query on PGV

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GA [auth A]
HA [auth A]
HB [auth N]
IB [auth N]
PA [auth C]
GA [auth A],
HA [auth A],
HB [auth N],
IB [auth N],
PA [auth C],
QA [auth C],
RB [auth P],
SB [auth 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
DMU
Query on DMU

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ZA [auth M],
ZB [auth Z]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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JA [auth B]
JB [auth O]
KA [auth C]
LA [auth C]
MB [auth P]
JA [auth B],
JB [auth O],
KA [auth C],
LA [auth C],
MB [auth P],
NB [auth P],
XA [auth J],
YB [auth W]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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IA [auth B],
LB [auth O]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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UA [auth F],
VB [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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AA [auth A],
AB [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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BA [auth A],
BB [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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CA [auth A],
CB [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX
Query on UNX

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RA [auth C],
TB [auth P]
UNKNOWN ATOM OR ION
X
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
G, T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
I, V
L-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

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Structure summary