8GCQ

SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Bos taurus
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTMMemProtMDmpstruc

  • Deposited: 2023-03-02 Released: 2023-09-27 
  • Deposition Author(s): Ishigami, I., Yeh, S.-R., Rousseau, D.L.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Structural insights into functional properties of the oxidized form of cytochrome c oxidase.

Ishigami, I.Sierra, R.G.Su, Z.Peck, A.Wang, C.Poitevin, F.Lisova, S.Hayes, B.Moss 3rd, F.R.Boutet, S.Sublett, R.E.Yoon, C.H.Yeh, S.R.Rousseau, D.L.

(2023) Nat Commun 14: 5752-5752

  • DOI: https://doi.org/10.1038/s41467-023-41533-x
  • Primary Citation of Related Structures:  
    8GCQ

  • PubMed Abstract: 

    Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable O H state, and a reductive phase, in which O H is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if O H is allowed to relax to the resting oxidized state (O), a redox equivalent to O H , its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a 3 iron and Cu B in the active site of the O state, like those in the O H state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from O H , where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00396 (Bos taurus)
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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 
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00415 (Bos taurus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00423 (Bos taurus)
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UniProt GroupP00423
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00426 (Bos taurus)
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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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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos 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
85Bos 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 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
59Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13183 (Bos taurus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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PA [auth C],
RA [auth C],
WB [auth P],
YB [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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BB [auth L]
GB [auth N]
IA [auth B]
LB [auth N]
NB [auth O]
BB [auth L],
GB [auth N],
IA [auth B],
LB [auth N],
NB [auth O],
VA [auth D]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA (Subject of Investigation/LOI)
Query on HEA

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EA [auth A],
FA [auth A],
IB [auth N],
JB [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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CC [auth T]
MA [auth C]
NA [auth C]
QB [auth P]
TB [auth P]
CC [auth T],
MA [auth C],
NA [auth C],
QB [auth P],
TB [auth P],
UA [auth C]
(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 (Subject of Investigation/LOI)
Query on PSC

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EC [auth V],
JA [auth B]
(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 (Subject of Investigation/LOI)
Query on PGV

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DA [auth A]
HB [auth N]
KA [auth C]
MB [auth N]
OA [auth C]
DA [auth A],
HB [auth N],
KA [auth C],
MB [auth N],
OA [auth C],
UB [auth P],
VB [auth P],
YA [auth H]
(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 (Subject of Investigation/LOI)
Query on DMU

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CB [auth M]
RB [auth P]
SA [auth C]
TA [auth C]
XA [auth G]
CB [auth M],
RB [auth P],
SA [auth C],
TA [auth C],
XA [auth G],
ZB [auth Q]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD (Subject of Investigation/LOI)
Query on CHD

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AB [auth J]
BC [auth T]
DC [auth T]
GC [auth W]
HC [auth Y]
AB [auth J],
BC [auth T],
DC [auth T],
GC [auth W],
HC [auth Y],
LA [auth C],
PB [auth O],
QA [auth C],
SB [auth P],
XB [auth P]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
SAC (Subject of Investigation/LOI)
Query on SAC

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FC [auth V],
ZA [auth I]
N-ACETYL-SERINE
C5 H9 N O4
JJIHLJJYMXLCOY-BYPYZUCNSA-N
CUA
Query on CUA

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

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

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AA [auth A],
DB [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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BA [auth A],
EB [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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CA [auth A],
FB [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
OH
Query on OH

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GA [auth A],
KB [auth N]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
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: 2.38 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.6α = 90
b = 189.5β = 90
c = 211.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1404929
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM126297
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115773
Department of Energy (DOE, United States)United StatesDE-AC02- 76SF00515
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesS10OD023453
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM139687

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release