7YPY

Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5B1A


Literature

The Mg2+-containing water cluster of mammalian cytochrome c oxidase collects four pumping proton equivalents in each catalytic cycle.

Yano, N.Muramoto, K.Shimada, A.Shinzawa-Itoh, K.Tsukihara, T.Yoshikawa, S.

(2016) J Biol Chem 291: 23882-23894

  • DOI: 10.1074/jbc.M115.711770
  • Primary Citation of Related Structures:  
    5B1A, 5B1B, 7YPY

  • PubMed Abstract: 
  • Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H 3 O + through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O 2 bound to heme a 3 To block backward proton movement, the water channel remains closed after O 2 binding until the sequential four-proton pumping process is complete ...

    Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H 3 O + through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O 2 bound to heme a 3 To block backward proton movement, the water channel remains closed after O 2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O 2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg 2+ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu 198 , which bridges the Mg 2+ and Cu A (the initial electron acceptor from cytochrome c) sites, suggest that the Cu A -Glu 198 -Mg 2+ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg 2+ -containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO.


    Organizational Affiliation

    From the Picobiology Institute and yoshi@sci.u-hyogo.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A, N514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B, O227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C, P261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialD, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialE, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
Membrane Entity: Yes 
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UniProt GroupP00426
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialF, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialG85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
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UniProt GroupP07471
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1H, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CI, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialJ, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialK, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialL, Y47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialM, Z46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialT85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
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UniProt GroupP07471
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Small Molecules
Ligands 16 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
BF [auth P],
DG [auth T],
MB [auth C],
TC [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
TGL (Subject of Investigation/LOI)
Query on TGL

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CB [auth B],
DC [auth D],
IA [auth A],
PF [auth Q],
SE [auth O],
CB [auth B],
DC [auth D],
IA [auth A],
PF [auth Q],
SE [auth O],
SG [auth Y]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
HEA (Subject of Investigation/LOI)
Query on HEA

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AA [auth A],
BA [auth A],
UD [auth N],
VD [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEK (Subject of Investigation/LOI)
Query on PEK

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CG [auth T],
FF [auth P],
PB [auth C],
RB [auth C],
TB [auth C],
CG [auth T],
FF [auth P],
PB [auth C],
RB [auth C],
TB [auth C],
ZE [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
 Ligand Interaction
PSC (Subject of Investigation/LOI)
Query on PSC

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FB [auth B],
VE [auth O]
(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
 Ligand Interaction
PGV (Subject of Investigation/LOI)
Query on PGV

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AE [auth N],
AF [auth P],
GA [auth A],
HA [auth A],
LB [auth C],
AE [auth N],
AF [auth P],
GA [auth A],
HA [auth A],
LB [auth C],
OF [auth Q],
QB [auth C],
UC [auth G]
(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
 Ligand Interaction
DMU (Subject of Investigation/LOI)
Query on DMU

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AC [auth C],
AD [auth I],
BB [auth A],
BC [auth C],
CC [auth C],
AC [auth C],
AD [auth I],
BB [auth A],
BC [auth C],
CC [auth C],
DF [auth P],
GD [auth K],
HD [auth K],
IC [auth D],
ID [auth K],
JD [auth K],
KD [auth K],
LD [auth K],
MF [auth P],
MG [auth X],
NF [auth P],
NG [auth X],
OG [auth X],
PG [auth X],
QD [auth L],
QG [auth X],
RD [auth M],
RG [auth X],
SB [auth C],
WG [auth Z],
YE [auth O]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD
Query on CHD

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CF [auth P],
EB [auth B],
EF [auth P],
LG [auth X],
NB [auth C],
CF [auth P],
EB [auth B],
EF [auth P],
LG [auth X],
NB [auth C],
OB [auth C],
PD [auth L],
UE [auth O],
VG [auth Y]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
CUA
Query on CUA

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DB [auth B],
TE [auth O]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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IG [auth U],
ZC [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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MC [auth F],
TF [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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

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AB [auth A],
AG [auth S],
BD [auth J],
BE [auth N],
BG [auth S],
AB [auth A],
AG [auth S],
BD [auth J],
BE [auth N],
BG [auth S],
CD [auth J],
CE [auth N],
DD [auth J],
DE [auth N],
EC [auth D],
ED [auth J],
EE [auth N],
EG [auth T],
FC [auth D],
FD [auth J],
FE [auth N],
FG [auth T],
GB [auth B],
GC [auth D],
GE [auth N],
GF [auth P],
GG [auth T],
HB [auth B],
HC [auth D],
HE [auth N],
HF [auth P],
HG [auth T],
IB [auth B],
IE [auth N],
IF [auth P],
JA [auth A],
JB [auth B],
JC [auth E],
JE [auth N],
JF [auth P],
JG [auth V],
KA [auth A],
KB [auth B],
KC [auth E],
KE [auth N],
KF [auth P],
KG [auth W],
LA [auth A],
LC [auth E],
LE [auth N],
LF [auth P],
MA [auth A],
MD [auth L],
ME [auth N],
NA [auth A],
NC [auth F],
ND [auth L],
NE [auth N],
OA [auth A],
OC [auth F],
OD [auth L],
OE [auth N],
PA [auth A],
PC [auth F],
PE [auth N],
QA [auth A],
QC [auth F],
QE [auth N],
QF [auth Q],
RA [auth A],
RC [auth F],
RE [auth N],
RF [auth Q],
SA [auth A],
SC [auth F],
SD [auth M],
SF [auth R],
TA [auth A],
TD [auth M],
TG [auth Y],
UA [auth A],
UB [auth C],
UF [auth S],
UG [auth Y],
VA [auth A],
VB [auth C],
VC [auth G],
VF [auth S],
WA [auth A],
WB [auth C],
WC [auth G],
WE [auth O],
WF [auth S],
XA [auth A],
XB [auth C],
XC [auth G],
XE [auth O],
XF [auth S],
XG [auth Z],
YA [auth A],
YB [auth C],
YC [auth H],
YF [auth S],
ZA [auth A],
ZB [auth C],
ZF [auth S]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

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FA [auth A],
ZD [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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EA [auth A],
YD [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, N L-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
G 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: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.938α = 90
b = 204.4β = 90
c = 177.896γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

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)Japan18K06092
Japan Society for the Promotion of Science (JSPS)Japan18K14635

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release