7VUW

Bovine heart cytochrome c oxidase in the cyanide-bound fully oxidized state at 50 K

  • Classification: OXIDOREDUCTASE
  • Organism(s): Bos taurus
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2021-11-04 Released: 2022-11-16 
  • Deposition Author(s): Shimada, A., Tsukihara, T.
  • Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons.

Shimada, A.Baba, J.Nagao, S.Shinzawa-Itoh, K.Yamashita, E.Muramoto, K.Tsukihara, T.Yoshikawa, S.

(2023) J Biol Chem 299: 105277-105277

  • DOI: https://doi.org/10.1016/j.jbc.2023.105277
  • Primary Citation of Related Structures:  
    7VUW, 7VVR, 7W3E

  • PubMed Abstract: 

    Cytochrome c oxidase (CcO) reduces O 2 in the O 2 -reduction site by sequential four-electron donations through the low-potential metal sites (Cu A and Fe a ). Redox-coupled X-ray crystal structural changes have been identified at five distinct sites including Asp 51 , Arg 438 , Glu 198 , the hydroxyfarnesyl ethyl group of heme a, and Ser 382 , respectively. These sites interact with the putative proton-pumping H-pathway. However, the metal sites responsible for each structural change have not been identified, since these changes were detected as structural differences between the fully reduced and fully oxidized CcOs. Thus, the roles of these structural changes in the CcO function are yet to be revealed. X-ray crystal structures of cyanide-bound CcOs under various oxidation states showed that the O 2 -reduction site controlled only the Ser 382 -including site, while the low-potential metal sites induced the other changes. This finding indicates that these low-potential site-inducible structural changes are triggered by sequential electron-extraction from the low-potential sites by the O 2 -reduction site and that each structural change is insensitive to the oxidation and ligand-binding states of the O 2 -reduction site. Because the proton/electron coupling efficiency is constant (1:1), regardless of the reaction progress in the O 2 -reduction site, the structural changes induced by the low-potential sites are assignable to those critically involved in the proton pumping, suggesting that the H-pathway, facilitating these low-potential site-inducible structural changes, pumps protons. Furthermore, a cyanide-bound CcO structure suggests that a hypoxia-inducible activator, Higd1a, activates the O 2 -reduction site without influencing the electron transfer mechanism through the low-potential sites, kinetically confirming that the low-potential sites facilitate proton pump.


  • Organizational Affiliation

    Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan.


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
Membrane Entity: Yes 
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
Membrane Entity: Yes 
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
259Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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
144Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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, mitochondrial
E, R
105Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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
94Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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
84Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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
79Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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 
Membrane Entity: Yes 
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, mitochondrial
J, W
58Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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
49Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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
43Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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 
AF [auth G],
PC [auth C],
WK [auth T],
YI [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

Download Ideal Coordinates CCD File 
LB [auth B]
MB [auth B]
SL [auth Y]
TJ [auth Q]
WG [auth N]
LB [auth B],
MB [auth B],
SL [auth Y],
TJ [auth Q],
WG [auth N],
ZF [auth L]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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

Download Ideal Coordinates CCD File 
KC [auth C]
LC [auth C]
MC [auth C]
TI [auth P]
UI [auth P]
KC [auth C],
LC [auth C],
MC [auth C],
TI [auth P],
UI [auth P],
VI [auth P]
(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 
AI [auth O],
OB [auth B]
(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 
GA [auth A]
HA [auth A]
NC [auth C]
OC [auth C]
WI [auth P]
GA [auth A],
HA [auth A],
NC [auth C],
OC [auth C],
WI [auth P],
XG [auth N],
XI [auth P],
YG [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 
AJ [auth P]
AM [auth Z]
BI [auth O]
BJ [auth P]
KG [auth M]
AJ [auth P],
AM [auth Z],
BI [auth O],
BJ [auth P],
KG [auth M],
OL [auth X],
PL [auth X],
QF [auth J],
QL [auth X],
RC [auth C],
RL [auth X],
SC [auth C],
XK [auth T],
ZG [auth N]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

Download Ideal Coordinates CCD File 
BF [auth G]
JC [auth C]
PB [auth B]
QC [auth C]
SI [auth P]
BF [auth G],
JC [auth C],
PB [auth B],
QC [auth C],
SI [auth P],
TL [auth Y],
ZI [auth P]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

Download Ideal Coordinates CCD File 
NB [auth B],
ZH [auth O]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GL [auth U],
JF [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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

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

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth B]
AD [auth C]
AE [auth D]
AG [auth L]
AB [auth A],
AC [auth B],
AD [auth C],
AE [auth D],
AG [auth L],
AH [auth N],
AK [auth Q],
AL [auth T],
BB [auth A],
BC [auth B],
BD [auth C],
BE [auth D],
BG [auth L],
BH [auth N],
BK [auth Q],
BL [auth T],
BM [auth Z],
CB [auth A],
CC [auth B],
CD [auth C],
CE [auth D],
CF [auth G],
CG [auth L],
CH [auth N],
CI [auth O],
CJ [auth P],
CK [auth R],
CL [auth T],
DB [auth A],
DC [auth B],
DD [auth C],
DE [auth D],
DF [auth G],
DG [auth L],
DH [auth N],
DI [auth O],
DJ [auth P],
DK [auth R],
DL [auth U],
EB [auth A],
EC [auth B],
ED [auth C],
EE [auth E],
EF [auth G],
EG [auth L],
EH [auth N],
EI [auth O],
EJ [auth P],
EK [auth R],
EL [auth U],
FB [auth A],
FC [auth B],
FD [auth C],
FE [auth E],
FF [auth H],
FG [auth L],
FH [auth N],
FI [auth O],
FJ [auth P],
FK [auth R],
FL [auth U],
GB [auth A],
GC [auth B],
GD [auth C],
GE [auth E],
GF [auth H],
GG [auth L],
GH [auth N],
GI [auth O],
GJ [auth P],
GK [auth R],
HB [auth A],
HC [auth B],
HD [auth C],
HE [auth E],
HF [auth H],
HG [auth L],
HH [auth N],
HI [auth O],
HJ [auth P],
HK [auth R],
HL [auth V],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth C],
IE [auth E],
IF [auth H],
IG [auth L],
IH [auth N],
II [auth O],
IJ [auth P],
IL [auth V],
JA [auth A],
JB [auth A],
JD [auth D],
JE [auth E],
JG [auth L],
JH [auth N],
JI [auth O],
JJ [auth P],
JK [auth S],
JL [auth V],
KA [auth A],
KB [auth A],
KD [auth D],
KE [auth E],
KF [auth I],
KH [auth N],
KI [auth O],
KJ [auth P],
KK [auth S],
KL [auth W],
LA [auth A],
LD [auth D],
LE [auth E],
LF [auth I],
LG [auth M],
LH [auth N],
LI [auth O],
LJ [auth P],
LK [auth S],
LL [auth W],
MA [auth A],
MD [auth D],
ME [auth E],
MF [auth I],
MG [auth M],
MH [auth N],
MI [auth O],
MJ [auth P],
MK [auth S],
ML [auth W],
NA [auth A],
ND [auth D],
NE [auth E],
NF [auth I],
NG [auth M],
NH [auth N],
NI [auth O],
NJ [auth P],
NK [auth S],
NL [auth W],
OA [auth A],
OD [auth D],
OE [auth E],
OF [auth I],
OG [auth M],
OH [auth N],
OI [auth O],
OJ [auth P],
OK [auth S],
PA [auth A],
PD [auth D],
PE [auth E],
PF [auth I],
PG [auth M],
PH [auth N],
PI [auth O],
PJ [auth P],
PK [auth S],
QA [auth A],
QB [auth B],
QD [auth D],
QE [auth E],
QH [auth N],
QI [auth O],
QJ [auth P],
QK [auth S],
RA [auth A],
RB [auth B],
RD [auth D],
RF [auth J],
RH [auth N],
RI [auth O],
RJ [auth P],
RK [auth S],
SA [auth A],
SB [auth B],
SD [auth D],
SE [auth F],
SF [auth J],
SH [auth N],
SJ [auth P],
SK [auth S],
TA [auth A],
TB [auth B],
TC [auth C],
TD [auth D],
TE [auth F],
TF [auth J],
TH [auth N],
TK [auth S],
UA [auth A],
UB [auth B],
UC [auth C],
UD [auth D],
UE [auth F],
UF [auth K],
UH [auth N],
UJ [auth Q],
UK [auth S],
UL [auth Y],
VA [auth A],
VB [auth B],
VC [auth C],
VD [auth D],
VE [auth F],
VF [auth K],
VH [auth N],
VJ [auth Q],
VK [auth S],
VL [auth Y],
WA [auth A],
WB [auth B],
WC [auth C],
WD [auth D],
WE [auth F],
WF [auth K],
WH [auth N],
WJ [auth Q],
WL [auth Y],
XA [auth A],
XB [auth B],
XC [auth C],
XD [auth D],
XE [auth F],
XF [auth K],
XH [auth N],
XJ [auth Q],
XL [auth Y],
YA [auth A],
YB [auth B],
YC [auth C],
YD [auth D],
YE [auth F],
YF [auth K],
YH [auth N],
YJ [auth Q],
YK [auth T],
YL [auth Y],
ZA [auth A],
ZB [auth B],
ZC [auth C],
ZD [auth D],
ZE [auth F],
ZJ [auth Q],
ZK [auth T],
ZL [auth Y]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CYN
Query on CYN

Download Ideal Coordinates CCD File 
FA [auth A],
VG [auth N]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
MG
Query on MG

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

Download Ideal Coordinates CCD File 
EA [auth A],
UG [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: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.076α = 90
b = 204.481β = 90
c = 177.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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 Science (JSPS)Japan18K06092
Japan Society for the Promotion of Science (JSPS)Japan15K18493
Japan Society for the Promotion of Science (JSPS)Japan18K14635
Japan Society for the Promotion of Science (JSPS)Japan26291033
Japan Science and TechnologyJapan12101577

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-01-17
    Changes: Database references