5B1B | pdb_00005b1b

Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

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.Takemura, S.Baba, J.Fujisawa, H.Mochizuki, M.Shinzawa-Itoh, K.Yamashita, E.Tsukihara, T.Yoshikawa, S.

(2016) J Biological Chem 291: 23882-23894

  • DOI: https://doi.org/10.1074/jbc.M115.711770
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 449.06 kDa 
  • Atom Count: 34,425 
  • Modeled Residue Count: 3,558 
  • Deposited Residue Count: 3,558 
  • 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 
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 
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
259Bos taurusMutation(s): 0 
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
144Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00423
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Reference Sequence
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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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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
98Bos taurusMutation(s): 0 
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
84Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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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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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
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, mitochondrial
J, W
58Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
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Reference Sequence
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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 
UniProt
Find proteins for P13183 (Bos taurus)
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UniProt GroupP13183
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Reference Sequence
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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 
UniProt
Find proteins for P00430 (Bos taurus)
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UniProt GroupP00430
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Reference Sequence
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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 
UniProt
Find proteins for P10175 (Bos taurus)
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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
BB [auth C],
PE [auth T],
VD [auth P],
YB [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL

Query on TGL



Download:Ideal Coordinates CCD File
EE [auth Q]
HA [auth A]
KD [auth O]
MB [auth D]
MC [auth L]
EE [auth Q],
HA [auth A],
KD [auth O],
MB [auth D],
MC [auth L],
WC [auth N]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA

Query on HEA



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
DB [auth C]
FB [auth C]
RD [auth P]
XB [auth G]
YD [auth P]
DB [auth C],
FB [auth C],
RD [auth P],
XB [auth G],
YD [auth P],
ZD [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



Download:Ideal Coordinates CCD File
IA [auth A],
MD [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
PGV

Query on PGV



Download:Ideal Coordinates CCD File
AB [auth C]
EB [auth C]
FA [auth A]
GA [auth A]
SD [auth P]
AB [auth C],
EB [auth C],
FA [auth A],
GA [auth A],
SD [auth P],
UC [auth N],
UD [auth P],
VC [auth N]
(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 X]
CF [auth Z]
DC [auth J]
GB [auth C]
AE [auth P],
AF [auth X],
CF [auth Z],
DC [auth J],
GB [auth C],
GC [auth K],
HC [auth K],
IC [auth K],
JC [auth K],
KC [auth K],
LC [auth K],
NB [auth D],
NC [auth L],
ND [auth O],
OB [auth D],
OC [auth M],
TD [auth P],
TE [auth W],
WE [auth X],
XE [auth X],
YE [auth X],
ZA [auth C],
ZE [auth X]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD

Query on CHD



Download:Ideal Coordinates CCD File
CB [auth C]
CC [auth J]
UA [auth B]
WD [auth P]
XD [auth P]
CB [auth C],
CC [auth J],
UA [auth B],
WD [auth P],
XD [auth P],
ZB [auth G]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA

Query on CUA



Download:Ideal Coordinates CCD File
LD [auth O],
TA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
BC [auth H],
SE [auth U]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
JE [auth S],
RB [auth F]
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



Download:Ideal Coordinates CCD File
AC [auth G]
AD [auth N]
BD [auth N]
BE [auth P]
BF [auth Y]
AC [auth G],
AD [auth N],
BD [auth N],
BE [auth P],
BF [auth Y],
CD [auth N],
CE [auth P],
DD [auth N],
DE [auth P],
EC [auth J],
ED [auth N],
FC [auth J],
FD [auth N],
FE [auth Q],
GD [auth N],
GE [auth Q],
HB [auth C],
HD [auth N],
HE [auth Q],
IB [auth C],
ID [auth N],
IE [auth R],
JA [auth A],
JB [auth C],
JD [auth N],
KA [auth A],
KB [auth C],
KE [auth S],
LA [auth A],
LB [auth C],
LE [auth S],
MA [auth A],
ME [auth S],
NA [auth A],
NE [auth S],
OA [auth A],
OD [auth O],
OE [auth S],
PA [auth A],
PB [auth E],
PD [auth O],
QA [auth A],
QB [auth E],
QD [auth O],
QE [auth T],
RA [auth A],
RE [auth T],
SA [auth A],
SB [auth F],
TB [auth F],
UB [auth F],
UE [auth W],
VA [auth B],
VB [auth F],
VE [auth W],
WA [auth B],
WB [auth F],
XA [auth B],
XC [auth N],
YA [auth B],
YC [auth N],
ZC [auth N]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth A],
SC [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
EA [auth A],
TC [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.606α = 90
b = 204.14β = 90
c = 177.653γ = 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
Ministry of Science, Education and Sports of the Republic of CroatiaJapan2247012
Japan Society for the Promotion of Science (JSPS)Japan22370060
Japan Society for the Promotion of Science (JSPS)Japan26291033

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-23
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2021-10-13
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Refinement description