2DYR

Bovine heart cytochrome C oxidase at the fully oxidized state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 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

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: 10.1038/sj.emboj.7601618
  • Primary Citation of Related Structures:  

  • 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 l ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
Gene Names: MT-CO1 (COI, COXI, MTCO1)
EC: 1.9.3.1
Find proteins for P00396 (Bos taurus)
Go to Gene View: MT-CO1
Go to UniProtKB:  P00396
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
Gene Names: MT-CO2 (COII, COX2, COXII, MTCO2)
Find proteins for P68530 (Bos taurus)
Go to Gene View: MT-CO2
Go to UniProtKB:  P68530
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
Gene Names: MT-CO3 (COIII, COXIII, MTCO3)
Find proteins for P00415 (Bos taurus)
Go to Gene View: MT-CO3
Go to UniProtKB:  P00415
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 4 isoform 1
D, Q
147Bos taurusMutation(s): 0 
Gene Names: COX4I1 (COX4)
Find proteins for P00423 (Bos taurus)
Go to Gene View: COX4I1
Go to UniProtKB:  P00423
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide Va
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
Find proteins for P00426 (Bos taurus)
Go to Gene View: COX5A
Go to UniProtKB:  P00426
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide Vb
F, S
98Bos taurusMutation(s): 0 
Gene Names: COX5B
Find proteins for P00428 (Bos taurus)
Go to Gene View: COX5B
Go to UniProtKB:  P00428
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIa-heart
G, T
85Bos taurusMutation(s): 0 
Gene Names: COX6A2 (COX6A)
Find proteins for P07471 (Bos taurus)
Go to Gene View: COX6A2
Go to UniProtKB:  P07471
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit VIb isoform 1
H, U
85Bos taurusMutation(s): 0 
Gene Names: COX6B1 (COX6B)
Find proteins for P00429 (Bos taurus)
Go to Gene View: COX6B1
Go to UniProtKB:  P00429
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIc
I, V
73Bos taurusMutation(s): 0 
Gene Names: COX6C
Find proteins for P04038 (Bos taurus)
Go to Gene View: COX6C
Go to UniProtKB:  P04038
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIIa-heart
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1 (COX7A, COX7AH)
Find proteins for P07470 (Bos taurus)
Go to Gene View: COX7A1
Go to UniProtKB:  P07470
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIIb
K, X
56Bos taurusMutation(s): 0 
Gene Names: COX7B
Find proteins for P13183 (Bos taurus)
Go to Gene View: COX7B
Go to UniProtKB:  P13183
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIIc
L, Y
47Bos taurusMutation(s): 0 
Gene Names: COX7C (COX7CP1)
Find proteins for P00430 (Bos taurus)
Go to Gene View: COX7C
Go to UniProtKB:  P00430
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIII-heart
M, Z
46Bos taurusMutation(s): 0 
Gene Names: COX8B (COX8H)
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download SDF File 
Download CCD File 
A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PEK
Query on PEK

Download SDF File 
Download CCD File 
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
PHOSPHATIDYLETHANOLAMINE, 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
 Ligand Interaction
CDL
Query on CDL

Download SDF File 
Download CCD File 
C, G, P, T
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
DMU
Query on DMU

Download SDF File 
Download CCD File 
C, M, P, Z
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
C, P
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
CUA
Query on CUA

Download SDF File 
Download CCD File 
B, O
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
CHD
Query on CHD

Download SDF File 
Download CCD File 
B, C, J, O, P, W
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
PSC
Query on PSC

Download SDF File 
Download CCD File 
B, 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
PHOSPHATIDYLCHOLINE, 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, N
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
TGL
Query on TGL

Download SDF File 
Download CCD File 
B, D, L, N, Q
TRISTEAROYLGLYCEROL
TRIACYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
PGV
Query on PGV

Download SDF File 
Download CCD File 
A, C, N, P, Z
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, B, N, O
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER
TPO
Query on TPO
G, T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 182.590α = 90.00
b = 205.140β = 90.00
c = 178.250γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance