5XDQ | pdb_00005xdq

Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.190 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.

Luo, F., Shinzawa-Itoh, K., Hagimoto, K., Shimada, A., Shimada, S., Yamashita, E., Yoshikawa, S., Tsukihara, T.

(2017) Acta Crystallogr F Struct Biol Commun 73: 416-422

  • DOI: https://doi.org/10.1107/S2053230X17008834
  • Primary Citation Related Structures: 
    5XDQ

  • PubMed Abstract: 

    Cytochrome c oxidase (CcO) couples proton pumping to O 2 reduction. Its enzymatic activity depends sensitively on pH over a wide range. However, owing to difficulty in crystallizing this protein, X-ray structure analyses of bovine CcO aimed at understanding its reaction mechanism have been conducted using crystals prepared at pH 5.7, which is significantly lower than that in the cell. Here, oxidized CcO at pH 7.3 was crystallized using a fluorinated octyl-maltoside derivative, and the structure was determined at 1.77 Å resolution. No structural differences between crystals obtained at the neutral pH and the acidic pH were detected within the molecules. On the other hand, some differences in intermolecular interactions were detected between the two types of crystal. The influence of pH on the molecular surface is likely to contribute to the pH dependency of the aerobic oxidation of ferrocytochrome c.

    • Organizational Affiliation: 
    • Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

Macromolecule Content 

  • Total Structure Weight: 446.41 kDa 
  • Atom Count: 34,218 
  • Modeled Residue Count: 3,550 
  • Deposited Residue Count: 3,606 
  • Unique protein chains: 13

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos 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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UniProt GroupP00396
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00423
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
94Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
59Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13183 (Bos taurus)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL


Download:Ideal Coordinates CCD File
AE [auth T],
FD [auth P],
IB [auth C],
UB [auth G]		CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL

Query on TGL


Download:Ideal Coordinates CCD File
BC [auth L]
OC [auth N]
OD [auth Q]
PB [auth D]
TA [auth B]
BC [auth L],
OC [auth N],
OD [auth Q],
PB [auth D],
TA [auth B],
XC [auth O]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA

Query on HEA


Download:Ideal Coordinates CCD File
AA [auth A],
BA [auth A],
JC [auth N],
KC [auth N]		HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK

Query on PEK


Download:Ideal Coordinates CCD File
DD [auth P]
EB [auth C]
FB [auth C]
WB [auth G]
YD [auth T]
DD [auth P],
EB [auth C],
FB [auth C],
WB [auth G],
YD [auth T],
ZD [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


Download:Ideal Coordinates CCD File
VA [auth B],
ZC [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


Download:Ideal Coordinates CCD File
DE [auth U]
ED [auth P]
FA [auth A]
GB [auth C]
HA [auth A]
DE [auth U],
ED [auth P],
FA [auth A],
GB [auth C],
HA [auth A],
HB [auth C],
PC [auth N],
RC [auth N]
(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


Download:Ideal Coordinates CCD File
GC [auth M]
HE [auth W]
JE [auth Z]
NB [auth C]
ND [auth P]
GC [auth M],
HE [auth W],
JE [auth Z],
NB [auth C],
ND [auth P],
OB [auth C]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD

Query on CHD


Download:Ideal Coordinates CCD File
BD [auth P]
CB [auth C]
EE [auth W]
GD [auth P]
JB [auth C]
BD [auth P],
CB [auth C],
EE [auth W],
GD [auth P],
JB [auth C],
VB [auth G],
WA [auth B],
ZB [auth J]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA

Query on CUA


Download:Ideal Coordinates CCD File
UA [auth B],
YC [auth O]		DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
RB [auth F],
UD [auth S]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU


Download:Ideal Coordinates CCD File
CA [auth A],
LC [auth N]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AB [auth B]
AC [auth J]
AD [auth O]
BB [auth B]
BE [auth T]
AB [auth B],
AC [auth J],
AD [auth O],
BB [auth B],
BE [auth T],
CC [auth L],
CE [auth T],
DC [auth L],
EC [auth L],
FC [auth L],
FE [auth W],
GE [auth W],
HC [auth M],
HD [auth P],
IA [auth A],
IC [auth M],
ID [auth P],
IE [auth Y],
JA [auth A],
JD [auth P],
KA [auth A],
KB [auth C],
KD [auth P],
LA [auth A],
LB [auth C],
LD [auth P],
MA [auth A],
MB [auth C],
MD [auth P],
NA [auth A],
OA [auth A],
PA [auth A],
PD [auth Q],
QA [auth A],
QB [auth E],
QD [auth R],
RA [auth A],
RD [auth R],
SA [auth A],
SB [auth F],
SC [auth N],
SD [auth R],
TB [auth F],
TC [auth N],
TD [auth R],
UC [auth N],
VC [auth N],
VD [auth S],
WC [auth N],
WD [auth S],
XA [auth B],
XB [auth G],
XD [auth S],
YA [auth B],
YB [auth H],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
PER

Query on PER


Download:Ideal Coordinates CCD File
GA [auth A],
QC [auth N]		PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
DA [auth A],
MC [auth N]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
CD [auth P],
DB [auth C],
EA [auth A],
NC [auth N]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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: 1.77 Å
  • R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.307α = 90
b = 205.904β = 90
c = 177.526γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JST CRESTJapanJPMJCR12M3

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary