6JY3

Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 ?
  • R-Value Free: 0.192 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Monomeric structure of an active form of bovine cytochromecoxidase.

Shinzawa-Itoh, K.Sugimura, T.Misaki, T.Tadehara, Y.Yamamoto, S.Hanada, M.Yano, N.Nakagawa, T.Uene, S.Yamada, T.Aoyama, H.Yamashita, E.Tsukihara, T.Yoshikawa, S.Muramoto, K.

(2019) Proc Natl Acad Sci U S A 116: 19945-19951

  • DOI: https://doi.org/10.1073/pnas.1907183116
  • Primary Citation of Related Structures:  
    6JY3, 6JY4

  • PubMed Abstract: 

    Cytochrome c oxidase (CcO), a membrane enzyme in the respiratory chain, catalyzes oxygen reduction by coupling electron and proton transfer through the enzyme with a proton pump across the membrane. In all crystals reported to date, bovine CcO exists as a dimer with the same intermonomer contacts, whereas CcOs and related enzymes from prokaryotes exist as monomers. Recent structural analyses of the mitochondrial respiratory supercomplex revealed that CcO monomer associates with complex I and complex III, indicating that the monomeric state is functionally important. In this study, we prepared monomeric and dimeric bovine CcO, stabilized using amphipol, and showed that the monomer had high activity. In addition, using a newly synthesized detergent, we determined the oxidized and reduced structures of monomer with resolutions of 1.85 and 1.95 ?, respectively. Structural comparison of the monomer and dimer revealed that a hydrogen bond network of water molecules is formed at the entry surface of the proton transfer pathway, termed the K-pathway, in monomeric CcO, whereas this network is altered in dimeric CcO. Based on these results, we propose that the monomer is the activated form, whereas the dimer can be regarded as a physiological standby form in the mitochondrial membrane. We also determined phospholipid structures based on electron density together with the anomalous scattering effect of phosphorus atoms. Two cardiolipins are found at the interface region of the supercomplex. We discuss formation of the monomeric CcO, dimeric CcO, and supercomplex, as well as their role in regulation of CcO activity.


  • Organizational Affiliation

    Graduate School of Life Science, University of Hyogo, Ako, 678-1297 Hyogo, Japan; shinzawa@sci.u-hyogo.ac.jp muramoto@sci.u-hyogo.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1514Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00396 (Bos taurus)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00396
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2227Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
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UniProt GroupP68530
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3261Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P00415 (Bos taurus)
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UniProt GroupP00415
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1147Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00423
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00426
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00428
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP07471
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B185Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00429
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP04038
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A159Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00430
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
GA [auth C],
S [auth A],
Y [auth B]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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N [auth A],
O [auth A]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

Download Ideal Coordinates CCD File 
EA [auth C](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
PGV
Query on PGV

Download Ideal Coordinates CCD File 
FA [auth C],
U [auth A]
(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
CHD (Subject of Investigation/LOI)
Query on CHD

Download Ideal Coordinates CCD File 
CA [auth C]CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CQX (Subject of Investigation/LOI)
Query on CQX

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
HA [auth C]
IA [auth C]
KA [auth G]
AA [auth B],
BA [auth B],
HA [auth C],
IA [auth C],
KA [auth G],
V [auth A],
W [auth A],
X [auth A]
(2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol
C18 H36 O7
VOSUWWUWOMLIMI-ZBRFXRBCSA-N
CUA
Query on CUA

Download Ideal Coordinates CCD File 
Z [auth B]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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JA [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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P [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
PER
Query on PER

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T [auth A]PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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Q [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth C],
R [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 ?
  • R-Value Free: 0.192 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 149.529¦Á = 90
b = 152.131¦Â = 90
c = 174.083¦Ã = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanKAKENHI Grant 117048028
Japan Society for the Promotion of ScienceJapanKAKENHI Grant 22570122
Japan Society for the Promotion of ScienceJapanKAKENHI Grant 17H03646
Japan Society for the Promotion of ScienceJapanKAKENHI Grant 22370060
Japan Society for the Promotion of ScienceJapanKAKENHI Grant 15K07029
Japan Society for the Promotion of ScienceJapanKAKENHI Grant 18K06162

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Structure summary
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