6NMP

SFX structure of oxidized cytochrome c oxidase at room temperature

  • Classification: OXIDOREDUCTASE
  • Organism(s): Bos taurus
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTMmpstruc

  • Deposited: 2019-01-11 Released: 2019-03-13 
  • Deposition Author(s): Rousseau, D.L., Yeh, S.-R., Ishigami, I.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Literature

Snapshot of an oxygen intermediate in the catalytic reaction of cytochromecoxidase.

Ishigami, I.Lewis-Ballester, A.Echelmeier, A.Brehm, G.Zatsepin, N.A.Grant, T.D.Coe, J.D.Lisova, S.Nelson, G.Zhang, S.Dobson, Z.F.Boutet, S.Sierra, R.G.Batyuk, A.Fromme, P.Fromme, R.Spence, J.C.H.Ros, A.Yeh, S.R.Rousseau, D.L.

(2019) Proc Natl Acad Sci U S A 116: 3572-3577

  • DOI: https://doi.org/10.1073/pnas.1814526116
  • Primary Citation of Related Structures:  
    6NKN, 6NMF, 6NMP

  • PubMed Abstract: 

    Cytochrome c oxidase (C c O) reduces dioxygen to water and harnesses the chemical energy to drive proton translocation across the inner mitochondrial membrane by an unresolved mechanism. By using time-resolved serial femtosecond crystallography, we identified a key oxygen intermediate of bovine C c O. It is assigned to the P R -intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a 3 iron atom is in a ferryl (Fe 4+ = O 2- ) configuration, and heme a and Cu B are oxidized while Cu A is reduced. A Helix-X segment is poised in an open conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a distinct structure. These data offer insights into the mechanism by which the oxygen chemistry is coupled to unidirectional proton translocation.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.


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 (PDB Primary Data), 7.1.1.9 (UniProt)
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 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
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UniProt GroupP68530
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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UniProt GroupP00415
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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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UniProt GroupP00426
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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
Find proteins for P07471 (Bos taurus)
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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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UniProt GroupP00429
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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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UniProt GroupP07470
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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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UniProt GroupP00430
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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RA [auth C],
SB [auth P],
WA [auth G],
YB [auth T]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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AB [auth L]
BC [auth Y]
HA [auth A]
MB [auth O]
YA [auth I]
AB [auth L],
BC [auth Y],
HA [auth A],
MB [auth O],
YA [auth I],
ZB [auth V]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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DA [auth A],
EA [auth A],
FB [auth N],
GB [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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PA [auth C]
PB [auth P]
TA [auth C]
VA [auth G]
XA [auth G]
PA [auth C],
PB [auth P],
TA [auth C],
VA [auth G],
XA [auth G],
XB [auth T]
(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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KA [auth B],
LB [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]
GA [auth A]
HB [auth N]
MA [auth C]
NB [auth P]
FA [auth A],
GA [auth A],
HB [auth N],
MA [auth C],
NB [auth P],
QA [auth C],
QB [auth P],
RB [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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BB [auth M],
NA [auth C],
UB [auth Q],
WB [auth T]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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AC [auth W]
KB [auth O]
LA [auth B]
OA [auth C]
OB [auth P]
AC [auth W],
KB [auth O],
LA [auth B],
OA [auth C],
OB [auth P],
SA [auth C],
TB [auth P],
ZA [auth J]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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

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

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

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IA [auth A],
IB [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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

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CA [auth A],
EB [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: 2.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.7α = 90
b = 189.8β = 90
c = 211.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098799
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095583
National Science Foundation (NSF, United States)United StatesSTC 1231306
National Science Foundation (NSF, United States)United StatesCHE-1404929
National Science Foundation (NSF, United States)United StatesBio ABI 1565180
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 2.0: 2019-03-20
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-11-27
    Changes: Author supporting evidence, Derived calculations
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary