7VVR

Bovine cytochrome c oxidese in CN-bound mixed valence state at 50 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

Starting Model: experimental
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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
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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 
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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 
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
259Bos taurusMutation(s): 0 
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
144Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00423
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
105Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00426
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
94Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
84Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP07471
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
79Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
58Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
49Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
43Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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LC [auth G],
NF [auth T],
OB [auth C],
QE [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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AB [auth B]
AF [auth Q]
GA [auth A]
KD [auth N]
VF [auth Y]
AB [auth B],
AF [auth Q],
GA [auth A],
KD [auth N],
VF [auth Y],
ZB [auth D]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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AA [auth A],
BA [auth A],
ED [auth N],
FD [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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KC [auth G]
LB [auth C]
LE [auth P]
ME [auth P]
MF [auth T]
KC [auth G],
LB [auth C],
LE [auth P],
ME [auth P],
MF [auth T],
NE [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

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CB [auth B],
EF [auth R]
(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

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HA [auth A]
IA [auth A]
LD [auth N]
MB [auth C]
MD [auth N]
HA [auth A],
IA [auth A],
LD [auth N],
MB [auth C],
MD [auth N],
NB [auth C],
OE [auth P],
PE [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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AD [auth L]
BD [auth M]
JE [auth O]
OC [auth G]
QF [auth T]
AD [auth L],
BD [auth M],
JE [auth O],
OC [auth G],
QF [auth T],
RC [auth J],
SE [auth P],
UC [auth K],
VC [auth K],
WC [auth K],
YB [auth C],
ZE [auth P],
ZF [auth Z]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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CE [auth O]
DB [auth B]
KB [auth C]
KE [auth P]
PB [auth C]
CE [auth O],
DB [auth B],
KB [auth C],
KE [auth P],
PB [auth C],
RE [auth P],
SC [auth J],
TF [auth W],
YF [auth Y],
ZC [auth L]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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BB [auth B],
DE [auth O]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4
Query on PO4

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QC [auth H],
SF [auth U]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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

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

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AC [auth D]
AE [auth N]
AG [auth Z]
BC [auth D]
BE [auth N]
AC [auth D],
AE [auth N],
AG [auth Z],
BC [auth D],
BE [auth N],
BF [auth Q],
CC [auth D],
CD [auth M],
CF [auth Q],
DC [auth E],
DD [auth M],
DF [auth Q],
EB [auth B],
EC [auth E],
EE [auth O],
FB [auth B],
FE [auth O],
FF [auth R],
GB [auth B],
GC [auth F],
GE [auth O],
GF [auth R],
HB [auth B],
HC [auth F],
HE [auth O],
IB [auth B],
IC [auth F],
IE [auth O],
IF [auth S],
JA [auth A],
JB [auth B],
JC [auth F],
JF [auth S],
KA [auth A],
KF [auth S],
LA [auth A],
LF [auth S],
MA [auth A],
MC [auth G],
NA [auth A],
NC [auth G],
ND [auth N],
OA [auth A],
OD [auth N],
OF [auth T],
PA [auth A],
PC [auth H],
PD [auth N],
PF [auth T],
QA [auth A],
QB [auth C],
QD [auth N],
RA [auth A],
RB [auth C],
RD [auth N],
RF [auth U],
SA [auth A],
SB [auth C],
SD [auth N],
TA [auth A],
TB [auth C],
TC [auth J],
TD [auth N],
TE [auth P],
UA [auth A],
UB [auth C],
UD [auth N],
UE [auth P],
UF [auth W],
VA [auth A],
VB [auth C],
VD [auth N],
VE [auth P],
WA [auth A],
WB [auth C],
WD [auth N],
WE [auth P],
WF [auth Y],
XA [auth A],
XB [auth C],
XC [auth L],
XD [auth N],
XE [auth P],
XF [auth Y],
YA [auth A],
YC [auth L],
YD [auth N],
YE [auth P],
ZA [auth A],
ZD [auth N]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CYN
Query on CYN

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FA [auth A],
JD [auth N]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
MG
Query on MG

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DA [auth A],
HD [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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EA [auth A],
ID [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: 1.65 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.307α = 90
b = 204.706β = 90
c = 177.379γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing

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)Japan26291033
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)Japan18K06092

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