8H8S

Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Reduced State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Calcium-bound structure of bovine cytochrome c oxidase.

Muramoto, K.Shinzawa-Itoh, K.

(2023) Biochim Biophys Acta Bioenerg 1864: 148956-148956

  • DOI: https://doi.org/10.1016/j.bbabio.2023.148956
  • Primary Citation of Related Structures:  
    8H8R, 8H8S

  • PubMed Abstract: 

    The crystal structure of bovine cytochrome c oxidase (CcO) shows a sodium ion (Na + ) bound to the surface of subunit I. Changes in the absorption spectrum of heme a caused by calcium ions (Ca 2+ ) are detected as small red shifts, and inhibition of enzymatic activity under low turnover conditions is observed by addition of Ca 2+ in a competitive manner with Na + . In this study, we determined the crystal structure of Ca 2+ -bound bovine CcO in the oxidized and reduced states at 1.7 Å resolution. Although Ca 2+ and Na + bound to the same site of oxidized and reduced CcO, they led to different coordination geometries. Replacement of Na + with Ca 2+ caused a small structural change in the loop segments near the heme a propionate and formyl groups, resulting in spectral changes in heme a. Redox-coupled structural changes observed in the Ca 2+ -bound form were the same as those previously observed in the Na + -bound form, suggesting that binding of Ca 2+ does not severely affect enzymatic function, which depends on these structural changes. The relation between the Ca 2+ binding and the inhibitory effect during slow turnover, as well as the possible role of bound Ca 2+ are discussed.


  • Organizational Affiliation

    Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, 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 
Gene Names: MT-CO1COICOXIMTCO1
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 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
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
261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
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
147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
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
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
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
98Bos taurusMutation(s): 0 
Gene Names: COX5B
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
85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
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
85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
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 
Gene Names: COX6C
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
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
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
56Bos taurusMutation(s): 0 
Gene Names: COX7B
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
47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
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
46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
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 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
AB [auth C]
FA [auth A]
JC [auth L]
PD [auth P]
VE [auth V]
AB [auth C],
FA [auth A],
JC [auth L],
PD [auth P],
VE [auth V],
XE [auth Y]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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

Download Ideal Coordinates CCD File 
DC [auth G],
QE [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 
BD [auth N],
NA [auth A],
OD [auth P],
ZA [auth C]
(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 
AE [auth P]
AF [auth Z]
BE [auth P]
CB [auth C]
CD [auth N]
AE [auth P],
AF [auth Z],
BE [auth P],
CB [auth C],
CD [auth N],
CE [auth P],
DE [auth P],
EC [auth G],
FC [auth G],
GD [auth O],
HA [auth A],
HC [auth H],
HE [auth P],
IA [auth A],
IC [auth J],
ID [auth O],
IE [auth Q],
JD [auth O],
KC [auth L],
KD [auth O],
LC [auth M],
MB [auth C],
MC [auth M],
NB [auth C],
OA [auth A],
OB [auth C],
PB [auth C],
QA [auth B],
QB [auth C],
RA [auth B],
RD [auth P],
SA [auth B],
TE [auth T],
UB [auth C],
UC [auth N],
VC [auth N],
WA [auth B],
WB [auth D],
WE [auth W],
YE [auth Y],
ZD [auth P],
ZE [auth Z]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

Download Ideal Coordinates CCD File 
BB [auth C]
DD [auth O]
MD [auth P]
QD [auth P]
UA [auth B]
BB [auth C],
DD [auth O],
MD [auth P],
QD [auth P],
UA [auth B],
XA [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
DB [auth C]
EB [auth C]
ED [auth O]
FB [auth C]
FD [auth O]
DB [auth C],
EB [auth C],
ED [auth O],
FB [auth C],
FD [auth O],
GA [auth A],
GB [auth C],
HB [auth C],
IB [auth C],
JB [auth C],
KB [auth C],
LB [auth C],
PE [auth T],
RE [auth T],
SC [auth N],
SD [auth P],
SE [auth T],
TC [auth N],
TD [auth P],
UD [auth P],
VA [auth B],
VB [auth C],
VD [auth P],
WD [auth P],
XD [auth P],
YD [auth P]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
CUA
Query on CUA

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

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

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

Download Ideal Coordinates CCD File 
AD [auth N]
BC [auth F]
CC [auth F]
EE [auth P]
FE [auth P]
AD [auth N],
BC [auth F],
CC [auth F],
EE [auth P],
FE [auth P],
GC [auth G],
GE [auth P],
JA [auth A],
JE [auth R],
KA [auth A],
KE [auth R],
LA [auth A],
LD [auth O],
LE [auth R],
MA [auth A],
NE [auth S],
OE [auth S],
RB [auth C],
SB [auth C],
TA [auth B],
TB [auth C],
UE [auth T],
WC [auth N],
XB [auth E],
XC [auth N],
YB [auth E],
YC [auth N],
ZB [auth E],
ZC [auth N]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
EA [auth A],
RC [auth N]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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

Download Ideal Coordinates CCD File 
ND [auth P],
YA [auth C]
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: 1.70 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.1α = 90
b = 204.7β = 90
c = 177.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18K06162
Japan Society for the Promotion of Science (JSPS)JapanJP17H03646
Japan Society for the Promotion of Science (JSPS)JapanJP22K06130
Other governmentJapanHyogo Science and Technology Association 4069

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-03-13
    Changes: Author supporting evidence, Refinement description, Structure summary
  • Version 2.0: 2024-03-20
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Structure summary