8H8S | pdb_00008h8s

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 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.124 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.125 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 460.02 kDa 
  • Atom Count: 33,023 
  • Modeled Residue Count: 3,474 
  • Deposited Residue Count: 3,614 
  • Unique protein chains: 13

Macromolecules

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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)
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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 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
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 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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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
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
Membrane Entity: Yes 
UniProt
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Reference Sequence
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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
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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 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
UniProt
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UniProt GroupP07471
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
Membrane Entity: Yes 
UniProt
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UniProt GroupP00429
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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 
Gene Names: COX6C
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
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
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UniProt GroupP07470
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Reference Sequence
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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)
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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 
Gene Names: COX7CCOX7CP1
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 
Gene Names: COX8BCOX8H
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
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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 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.124 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.125 (Depositor) 
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