7CP5

Bovine heart cytochrome c oxidase in a catalytic intermediate of E at 1.76 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates.

Shimada, A.Hara, F.Shinzawa-Itoh, K.Kanehisa, N.Yamashita, E.Muramoto, K.Tsukihara, T.Yoshikawa, S.

(2021) J Biol Chem 297: 100967-100967

  • DOI: https://doi.org/10.1016/j.jbc.2021.100967
  • Primary Citation of Related Structures:  
    7CP5, 7D5W, 7D5X

  • PubMed Abstract: 

    Mammalian cytochrome c oxidase (CcO) reduces O 2 to water in a bimetallic site including Fe a3 and Cu B giving intermediate molecules, termed A-, P-, F-, O-, E-, and R-forms. From the P-form on, each reaction step is driven by single-electron donations from cytochrome c coupled with the pumping of a single proton through the H-pathway, a proton-conducting pathway composed of a hydrogen-bond network and a water channel. The proton-gradient formed is utilized for ATP production by F-ATPase. For elucidation of the proton pumping mechanism, crystal structural determination of these intermediate forms is necessary. Here we report X-ray crystallographic analysis at ∼1.8 Å resolution of fully reduced CcO crystals treated with O 2 for three different time periods. Our disentanglement of intermediate forms from crystals that were composed of multiple forms determined that these three crystallographic data sets contained ∼45% of the O-form structure, ∼45% of the E-form structure, and ∼20% of an oxymyoglobin-type structure consistent with the A-form, respectively. The O- and E-forms exhibit an unusually long Cu B 2+ -OH - distance and Cu B 1+ -H 2 O structure keeping Fe a3 3+ -OH - state, respectively, suggesting that the O- and E-forms have high electron affinities that cause the O→E and E→R transitions to be essentially irreversible and thus enable tightly coupled proton pumping. The water channel of the H-pathway is closed in the O- and E-forms and partially open in the R-form. These structures, together with those of the recently reported P- and F-forms, indicate that closure of the H-pathway water channel avoids back-leaking of protons for facilitating the effective proton pumping.


  • Organizational Affiliation

    Picobiology Institute, Graduate School of Life Science, University of Hyogo, kamigori, Akoh, 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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UniProt GroupP68530
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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 
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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 
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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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BD [auth N],
BF [auth T],
DB [auth C],
FE [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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JD [auth N]
LD [auth N]
MD [auth N]
SA [auth B]
UB [auth D]
JD [auth N],
LD [auth N],
MD [auth N],
SA [auth B],
UB [auth D],
YC [auth L]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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

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EB [auth C]
FB [auth C]
GE [auth P]
HB [auth C]
HE [auth P]
EB [auth C],
FB [auth C],
GE [auth P],
HB [auth C],
HE [auth P],
JE [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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GA [auth A],
YD [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

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FA [auth A]
GB [auth C]
HD [auth N]
ID [auth N]
IE [auth P]
FA [auth A],
GB [auth C],
HD [auth N],
ID [auth N],
IE [auth P],
JB [auth C],
JC [auth G],
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

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AD [auth M]
BB [auth C]
EE [auth P]
GF [auth W]
IB [auth C]
AD [auth M],
BB [auth C],
EE [auth P],
GF [auth W],
IB [auth C],
IF [auth X],
JF [auth X],
KE [auth P],
KF [auth X],
LF [auth X],
NC [auth J],
PF [auth Z],
QC [auth K],
RC [auth K],
SC [auth K],
TB [auth D],
TC [auth K],
TE [auth Q],
UC [auth K],
VB [auth D],
VC [auth K],
WC [auth L],
XD [auth O]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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CB [auth C]
CE [auth P]
IC [auth G]
MF [auth Y]
UA [auth B]
CB [auth C],
CE [auth P],
IC [auth G],
MF [auth Y],
UA [auth B],
XC [auth L]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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

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

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

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

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AC [auth E]
AE [auth O]
AF [auth S]
BC [auth E]
BE [auth O]
AC [auth E],
AE [auth O],
AF [auth S],
BC [auth E],
BE [auth O],
CF [auth T],
DC [auth F],
DF [auth T],
EC [auth F],
EF [auth T],
FC [auth F],
GC [auth F],
HC [auth F],
HF [auth W],
IA [auth A],
JA [auth A],
KA [auth A],
KB [auth C],
KC [auth G],
LA [auth A],
LB [auth C],
LC [auth G],
LE [auth P],
MA [auth A],
MB [auth C],
ME [auth P],
NA [auth A],
NB [auth C],
ND [auth N],
NE [auth P],
NF [auth Y],
OA [auth A],
OB [auth C],
OC [auth J],
OD [auth N],
OE [auth P],
OF [auth Y],
PA [auth A],
PB [auth C],
PC [auth J],
PD [auth N],
PE [auth P],
QA [auth A],
QB [auth C],
QD [auth N],
QE [auth P],
RA [auth A],
RB [auth C],
RD [auth N],
RE [auth P],
SB [auth C],
SD [auth N],
SE [auth P],
TD [auth N],
UD [auth N],
UE [auth Q],
VA [auth B],
VD [auth N],
WA [auth B],
WB [auth D],
WE [auth S],
XA [auth B],
XB [auth D],
XE [auth S],
YA [auth B],
YB [auth D],
YE [auth S],
ZB [auth E],
ZC [auth L],
ZD [auth O],
ZE [auth S]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
PER
Query on PER

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HA [auth A],
KD [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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

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AB [auth C],
DE [auth P],
EA [auth A],
GD [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: 1.76 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.589α = 90
b = 203.218β = 90
c = 177.702γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2021-09-15
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description