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: 0.157 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

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This is version 1.2 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
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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
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UniProt GroupP00396
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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
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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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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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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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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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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
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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 
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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 
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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 
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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 
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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 
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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 
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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CB [auth C]
FA [auth A]
LC [auth L]
RD [auth P]
XE [auth V]
CB [auth C],
FA [auth A],
LC [auth L],
RD [auth P],
XE [auth V],
ZE [auth Y]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA (Subject of Investigation/LOI)
Query on HEA

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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

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GC [auth G],
TE [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

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BB [auth C],
DD [auth N],
NA [auth A],
QD [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

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AF [auth Y]
BE [auth P]
BF [auth Z]
CE [auth P]
CF [auth Z]
AF [auth Y],
BE [auth P],
BF [auth Z],
CE [auth P],
CF [auth Z],
DE [auth P],
EB [auth C],
ED [auth N],
EE [auth P],
FE [auth P],
HA [auth A],
HC [auth G],
IA [auth A],
IC [auth G],
ID [auth O],
JE [auth P],
KC [auth J],
KD [auth O],
LD [auth O],
LE [auth Q],
MC [auth L],
MD [auth O],
NC [auth M],
OA [auth A],
OB [auth C],
OC [auth M],
PA [auth A],
PB [auth C],
QB [auth C],
RA [auth B],
RB [auth C],
SA [auth B],
SB [auth C],
TA [auth B],
TD [auth P],
WB [auth C],
WC [auth N],
XA [auth B],
XC [auth N],
YA [auth B],
YE [auth W],
ZB [auth D]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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DB [auth C]
FD [auth O]
OD [auth P]
SD [auth P]
VA [auth B]
DB [auth C],
FD [auth O],
OD [auth P],
SD [auth P],
VA [auth B],
ZA [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
LFA
Query on LFA

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AE [auth P]
FB [auth C]
GA [auth A]
GB [auth C]
GD [auth O]
AE [auth P],
FB [auth C],
GA [auth A],
GB [auth C],
GD [auth O],
HB [auth C],
HD [auth O],
IB [auth C],
JB [auth C],
KB [auth C],
LB [auth C],
MB [auth C],
NB [auth C],
SE [auth T],
UC [auth N],
UD [auth P],
UE [auth T],
VC [auth N],
VD [auth P],
VE [auth T],
WA [auth B],
WD [auth P],
XB [auth C],
XD [auth P],
YD [auth P],
ZD [auth P]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
MES (Subject of Investigation/LOI)
Query on MES

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KE [auth Q],
YB [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CUA (Subject of Investigation/LOI)
Query on CUA

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JD [auth O],
QA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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DC [auth F],
PE [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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

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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],
EC [auth F],
FC [auth F],
GE [auth P],
HE [auth P],
IE [auth P],
JA [auth A],
JC [auth G],
KA [auth A],
LA [auth A],
MA [auth A],
ME [auth R],
ND [auth O],
NE [auth R],
OE [auth R],
QE [auth S],
RE [auth S],
TB [auth C],
UA [auth B],
UB [auth C],
VB [auth C],
WE [auth T],
YC [auth N],
ZC [auth N]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

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EA [auth A],
TC [auth N]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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DA [auth A],
SC [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX

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AB [auth C],
PD [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: 1.70 Å
  • R-Value Free: 0.157 
  • 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

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Ligand Structure Quality Assessment 


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
Hyogo Science and Technology AssociationJapan4069

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