6NKN image
Deposition Date 2019-01-07
Release Date 2019-03-20
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6NKN
Keywords:
OXIDOREDUCTASE
Title:
Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature
Biological Source:
Source Organism:
Bos taurus (Taxon ID: 9913)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.50 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
6NKN validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 1
Gene (Uniprot):MT-CO1
Chain IDs:A, N
Chain Length:514
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00396 Pfam ID:PF00115 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 2
Gene (Uniprot):MT-CO2
Chain IDs:B, O
Chain Length:227
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P68530 Pfam ID:PF02790, PF00116
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 3
Gene (Uniprot):MT-CO3
Chain IDs:C, P
Chain Length:261
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00415 Pfam ID:PF00510 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Gene (Uniprot):COX4I1
Chain IDs:D, Q
Chain Length:147
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00423 Pfam ID:PF02936 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5A, mitochondrial
Gene (Uniprot):COX5A
Chain IDs:E, R
Chain Length:109
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00426 Pfam ID:PF02284 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5B, mitochondrial
Gene (Uniprot):COX5B
Chain IDs:F, S
Chain Length:98
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00428 Pfam ID:PF01215 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6A2, mitochondrial
Gene (Uniprot):COX6A2
Chain IDs:G, T
Chain Length:85
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P07471 Pfam ID:PF02046 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6B1
Gene (Uniprot):COX6B1
Chain IDs:H, U
Chain Length:85
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00429 Pfam ID:PF02297 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6C
Gene (Uniprot):COX6C
Chain IDs:I, V
Chain Length:73
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P04038 Pfam ID:PF02937 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7A1, mitochondrial
Gene (Uniprot):COX7A1
Chain IDs:J, W
Chain Length:59
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P07470 Pfam ID:PF02238 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7B, mitochondrial
Gene (Uniprot):COX7B
Chain IDs:K, X
Chain Length:56
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P13183 Pfam ID:PF05392 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7C, mitochondrial
Gene (Uniprot):COX7C
Chain IDs:L, Y
Chain Length:47
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00430 Pfam ID:PF02935 EC:7.1.1.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 8B, mitochondrial
Gene (Uniprot):COX8B
Chain IDs:M, Z
Chain Length:46
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P10175 Pfam ID:PF02285 EC:7.1.1.9
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME A MET modified residue
SAC I SER modified residue
TPO G THR modified residue
Ligand Molecules
CDL
CHD
CU
CUA
DMU
HEA
MG
NA
O
OH
PEK
PGV
PSC
TGL
ZN
Primary Citation
Snapshot of an oxygen intermediate in the catalytic reaction of cytochromecoxidase.
Proc. Natl. Acad. Sci. U.S.A. 116 3572 3577 (2019)
PMID: 30808749 DOI: 10.1073/pnas.1814526116

Abstact

Cytochrome c oxidase (CcO) 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 CcO. It is assigned to the PR-intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a3 iron atom is in a ferryl (Fe4+ = O2-) configuration, and heme a and CuB are oxidized while CuA 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.

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Disease

Primary Citation of related structures
6NKN