2DYS

Bovine heart cytochrome C oxidase modified by DCCD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase

Shinzawa-Itoh, K.Aoyama, H.Muramoto, K.Terada, H.Kurauchi, T.Tadehara, Y.Yamasaki, A.Sugimura, T.Kurono, S.Tsujimoto, K.Mizushima, T.Yamashita, E.Tsukihara, T.Yoshikawa, S.

(2007) EMBO J 26: 1713-1725

  • DOI: https://doi.org/10.1038/sj.emboj.7601618
  • Primary Citation of Related Structures:  
    2DYR, 2DYS

  • PubMed Abstract: 

    All 13 lipids, including two cardiolipins, one phosphatidylcholine, three phosphatidylethanolamines, four phosphatidylglycerols and three triglycerides, were identified in a crystalline bovine heart cytochrome c oxidase (CcO) preparation. The chain lengths and unsaturated bond positions of the fatty acid moieties determined by mass spectrometry suggest that each lipid head group identifies its specific binding site within CcOs. The X-ray structure demonstrates that the flexibility of the fatty acid tails facilitates their effective space-filling functions and that the four phospholipids stabilize the CcO dimer. Binding of dicyclohexylcarbodiimide to the O(2) transfer pathway of CcO causes two palmitate tails of phosphatidylglycerols to block the pathway, suggesting that the palmitates control the O(2) transfer process.The phosphatidylglycerol with vaccenate (cis-Delta(11)-octadecenoate) was found in CcOs of bovine and Paracoccus denitrificans, the ancestor of mitochondrion, indicating that the vaccenate is conserved in bovine CcO in spite of the abundance of oleate (cis-Delta(9)-octadecenoate). The X-ray structure indicates that the protein moiety selects cis-vaccenate near the O(2) transfer pathway against trans-vaccenate. These results suggest that vaccenate plays a critical role in the O(2) transfer mechanism.


  • Organizational Affiliation

    Department of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
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 subunit 2
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 subunit 3
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 4 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 subunit VIb isoform 1
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 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BC [auth T],
TA [auth C],
XA [auth G],
XB [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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AB [auth L]
HB [auth N]
IA [auth B]
IB [auth N]
NB [auth O]
AB [auth L],
HB [auth N],
IA [auth B],
IB [auth N],
NB [auth O],
VA [auth D]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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

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AC [auth T]
PA [auth C]
QA [auth C]
TB [auth P]
UB [auth P]
AC [auth T],
PA [auth C],
QA [auth C],
TB [auth P],
UB [auth P],
YA [auth G]
(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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JA [auth B],
OB [auth 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
PGV
Query on PGV

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FA [auth A]
GA [auth A]
JB [auth N]
KB [auth N]
RA [auth C]
FA [auth A],
GA [auth A],
JB [auth N],
KB [auth N],
RA [auth C],
SA [auth C],
VB [auth P],
WB [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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BB [auth M],
DC [auth Z],
MA [auth C],
PB [auth P]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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CC [auth W]
KA [auth B]
MB [auth O]
OA [auth C]
SB [auth P]
CC [auth W],
KA [auth B],
MB [auth O],
OA [auth C],
SB [auth P],
UA [auth C],
YB [auth P],
ZA [auth J]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
DCW
Query on DCW

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LA [auth C],
RB [auth P]
DICYCLOHEXYLUREA
C13 H24 N2 O
ADFXKUOMJKEIND-UHFFFAOYSA-N
CUA
Query on CUA

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

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

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

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

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

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NA [auth C],
QB [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: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.13α = 90
b = 207.232β = 90
c = 178.242γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-23
    Changes: Non-polymer description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary