9IKF | pdb_00009ikf

Bovine Heart Cytochrome c Oxidase in the Carbon Dioxide-bound Fully Oxidized State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.167 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.130 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.132 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The binding sites of carbon dioxide, nitrous oxide, and xenon reveal a putative exhaust channel for bovine cytochrome c oxidase.

Muramoto, K.Ide, T.Shinzawa-Itoh, K.

(2025) J Biological Chem : 110395-110395

  • DOI: https://doi.org/10.1016/j.jbc.2025.110395
  • Primary Citation of Related Structures:  
    9IKF, 9IKG, 9IKH, 9IKI, 9KUK, 9KUL, 9KUM, 9M56

  • PubMed Abstract: 

    Cytochrome c oxidase (CcO) catalyzes oxygen (O 2 ) reduction at the heme a 3 -Cu B site in the transmembrane region of the enzyme. It has been proposed that the hydrophobic channel that connects the transmembrane surface of subunit III through subunit I to the heme a 3 -Cu B site is the O 2 transfer pathway. Gas molecules other than O 2 , including carbon dioxide (CO 2 ) generated in the TCA cycle, should also enter the hydrophobic channel, but it is not clear how these molecules are expelled from CcO. We analyzed the crystal structures of CO 2 -, nitrous oxide (N 2 O)-, and Xe-bound bovine CcO in the oxidized and reduced states at resolutions of 1.75-1.85 Å. Binding of Xe in the channel of subunit I near the interface with subunit III supported the proposed O 2 transfer pathway. CO 2 , N 2 O, and another Xe were all bound to a common site near the branching point of another hydrophobic channel that branched from the O 2 transport channel. Additional Xe atoms were bound in the second channel leading up to the molecular surface on the intermembrane space side, suggesting that under physiological conditions, CO 2 that has entered the O 2 pathway could be passively expelled through this channel. This channel consists of subunits I and nuclear DNA-coded subunit VIIc, suggesting that the addition of subunit VIIc in the process of molecular evolution of mitochondrial CcO has made the CO 2 exhaust pathway.


  • Organizational Affiliation

    Graduate School of Science, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo, Japan. Electronic address: muramoto@sci.u-hyogo.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P00396 (Bos taurus)
Explore P00396 
Go to UniProtKB:  P00396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00396
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P68530 (Bos taurus)
Explore P68530 
Go to UniProtKB:  P68530
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68530
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P00415 (Bos taurus)
Explore P00415 
Go to UniProtKB:  P00415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00415
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusMutation(s): 0 
UniProt
Find proteins for P00423 (Bos taurus)
Explore P00423 
Go to UniProtKB:  P00423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00423
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
UniProt
Find proteins for P00426 (Bos taurus)
Explore P00426 
Go to UniProtKB:  P00426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00426
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
98Bos taurusMutation(s): 0 
UniProt
Find proteins for P00428 (Bos taurus)
Explore P00428 
Go to UniProtKB:  P00428
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00428
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusMutation(s): 0 
UniProt
Find proteins for P07471 (Bos taurus)
Explore P07471 
Go to UniProtKB:  P07471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07471
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
UniProt
Find proteins for P00429 (Bos taurus)
Explore P00429 
Go to UniProtKB:  P00429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00429
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
UniProt
Find proteins for P04038 (Bos taurus)
Explore P04038 
Go to UniProtKB:  P04038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04038
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1
J, W
59Bos taurusMutation(s): 0 
UniProt
Find proteins for P07470 (Bos taurus)
Explore P07470 
Go to UniProtKB:  P07470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07470
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
56Bos taurusMutation(s): 0 
UniProt
Find proteins for P13183 (Bos taurus)
Explore P13183 
Go to UniProtKB:  P13183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13183
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
UniProt
Find proteins for P00430 (Bos taurus)
Explore P00430 
Go to UniProtKB:  P00430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00430
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
46Bos taurusMutation(s): 0 
UniProt
Find proteins for P10175 (Bos taurus)
Explore P10175 
Go to UniProtKB:  P10175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10175
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
BF [auth Y]
DB [auth C]
GA [auth A]
LC [auth L]
TD [auth P]
BF [auth Y],
DB [auth C],
GA [auth A],
LC [auth L],
TD [auth P],
ZE [auth V]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
PC [auth N],
QC [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

Download Ideal Coordinates CCD File 
GC [auth G],
VE [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
PGV
Query on PGV

Download Ideal Coordinates CCD File 
CB [auth C],
FD [auth N],
QA [auth A],
SD [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

Download Ideal Coordinates CCD File 
AF [auth W]
CF [auth Z]
DF [auth Z]
EE [auth P]
EF [auth Z]
AF [auth W],
CF [auth Z],
DF [auth Z],
EE [auth P],
EF [auth Z],
FB [auth C],
FE [auth P],
GE [auth P],
HC [auth G],
HE [auth P],
IE [auth P],
JC [auth H],
JD [auth O],
KA [auth A],
KC [auth J],
LA [auth A],
LD [auth O],
MC [auth L],
MD [auth O],
ME [auth P],
NC [auth M],
ND [auth O],
NE [auth P],
OB [auth C],
OC [auth M],
OE [auth Q],
PB [auth C],
QB [auth C],
RA [auth A],
RB [auth C],
SB [auth C],
TA [auth B],
UA [auth B],
VA [auth B],
VD [auth P],
WB [auth C],
XB [auth C],
YC [auth N],
YE [auth U],
ZA [auth B],
ZB [auth D],
ZC [auth N]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

Download Ideal Coordinates CCD File 
AB [auth C]
EB [auth C]
GD [auth O]
QD [auth P]
UD [auth P]
AB [auth C],
EB [auth C],
GD [auth O],
QD [auth P],
UD [auth P],
XA [auth B]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AE [auth P]
BE [auth P]
CE [auth P]
DE [auth P]
GB [auth C]
AE [auth P],
BE [auth P],
CE [auth P],
DE [auth P],
GB [auth C],
HB [auth C],
HD [auth O],
IA [auth A],
IB [auth C],
ID [auth O],
JA [auth A],
JB [auth C],
KB [auth C],
LB [auth C],
MB [auth C],
NB [auth C],
PD [auth P],
WC [auth N],
WD [auth P],
WE [auth T],
XC [auth N],
XD [auth P],
YA [auth B],
YB [auth C],
YD [auth P],
ZD [auth P]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
CUA
Query on CUA

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

Download Ideal Coordinates CCD File 
DC [auth F],
SE [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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

Download Ideal Coordinates CCD File 
AC [auth E]
AD [auth N]
BC [auth E]
BD [auth N]
CC [auth E]
AC [auth E],
AD [auth N],
BC [auth E],
BD [auth N],
CC [auth E],
CD [auth N],
DD [auth N],
EC [auth F],
ED [auth N],
FC [auth F],
IC [auth G],
JE [auth P],
KE [auth P],
LE [auth P],
MA [auth A],
NA [auth A],
OA [auth A],
OD [auth O],
PA [auth A],
PE [auth R],
QE [auth R],
RE [auth R],
TB [auth C],
TE [auth S],
UB [auth C],
UE [auth S],
VB [auth C],
WA [auth B],
XE [auth T]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO2 (Subject of Investigation/LOI)
Query on CO2

Download Ideal Coordinates CCD File 
HA [auth A],
VC [auth N]
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
PER
Query on PER

Download Ideal Coordinates CCD File 
FA [auth A],
UC [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth A],
SC [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth A],
TC [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
BB [auth C],
RD [auth P]
UNKNOWN ATOM OR ION
X
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.167 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.130 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.132 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.5α = 90
b = 204.4β = 90
c = 177.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata 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 Science (JSPS)Japan22K06130

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release