1V55

Bovine heart cytochrome c oxidase at the fully reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.230 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.210 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CDLClick on this verticalbar to view detailsBest fitted TGLClick on this verticalbar to view detailsBest fitted HEAClick on this verticalbar to view detailsBest fitted PEKClick on this verticalbar to view detailsBest fitted PSCClick on this verticalbar to view detailsBest fitted PGVClick on this verticalbar to view detailsBest fitted DMUClick on this verticalbar to view detailsBest fitted CHDClick on this verticalbar to view details

This is version 1.3 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: 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 (PDB Primary Data), 7.1.1.9 (UniProt)
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 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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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 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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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 
UniProt
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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 
UniProt
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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 
UniProt
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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

Download Ideal Coordinates CCD File 
OA [auth C],
OB [auth P],
WA [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]
GA [auth A]
GB [auth N]
HA [auth A]
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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PA [auth C]
PB [auth P]
QA [auth C]
QB [auth P]
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],
UA [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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HB [auth N]
IA [auth A]
IB [auth N]
JA [auth A]
RA [auth C]
(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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JB [auth O]
LA [auth B]
MA [auth C]
MB [auth P]
NA [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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

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VA [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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TA [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: 1.90 Å
  • R-Value Free:  0.230 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.06α = 90
b = 206.584β = 90
c = 178.298γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CDLClick on this verticalbar to view detailsBest fitted TGLClick on this verticalbar to view detailsBest fitted HEAClick on this verticalbar to view detailsBest fitted PEKClick on this verticalbar to view detailsBest fitted PSCClick on this verticalbar to view detailsBest fitted PGVClick on this verticalbar to view detailsBest fitted DMUClick on this verticalbar to view detailsBest fitted CHDClick on this verticalbar to view details

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: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary