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Crystal Structure of CO-bound Cytochrome c Oxidase determined by Synchrotron X-Ray Crystallography at 100 K

Source organism: Bos taurus
Biochemical function: cytochrome-c oxidase activity
Biological process: mitochondrial electron transport, cytochrome c to oxygen
Cellular component: mitochondrial respiratory chain complex IV

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EC 7.1.1.9: Cytochrome-c oxidase

Reaction catalysed:
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Systematic name:
Ferrocytochrome-c:oxygen oxidoreductase
Alternative Name(s):
  • Complex IV (mitochondrial electron transport)
  • Cytochrome a3
  • Cytochrome aa3
  • Cytochrome ba(3)
  • Cytochrome bb3
  • Cytochrome caa(3)
  • Cytochrome cbb(3)
  • Cytochrome oxidase
  • Ferrocytochrome c oxidase
  • Indophenol oxidase
  • Indophenolase
  • NADH cytochrome c oxidase
  • Warburg's respiratory enzyme

GO terms

Sequence families

Pfam Protein families (Pfam)
PF02285
Domain description: Cytochrome oxidase c subunit VIII
Occurring in:
  1. Cytochrome c oxidase subunit 8B, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02285 (Cytochrome oxidase c subunit VIII) in Cytochrome c oxidase subunit 8B, mitochondrial. Showing 1 copy in chain M.

PF02935
Domain description: Cytochrome c oxidase subunit VIIc
Occurring in:
  1. Cytochrome c oxidase subunit 7C, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02935 (Cytochrome c oxidase subunit VIIc) in Cytochrome c oxidase subunit 7C, mitochondrial. Showing 1 copy in chain L.

PF05392
Domain description: Cytochrome C oxidase chain VIIB
Occurring in:
  1. Cytochrome c oxidase subunit 7B, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF05392 (Cytochrome C oxidase chain VIIB) in Cytochrome c oxidase subunit 7B, mitochondrial. Showing 1 copy in chain K.

PF02238
Domain description: Cytochrome c oxidase subunit VII
Occurring in:
  1. Cytochrome c oxidase subunit 7A1, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02238 (Cytochrome c oxidase subunit VII) in Cytochrome c oxidase subunit 7A1, mitochondrial. Showing 1 copy in chain J.

PF02937
Domain description: Cytochrome c oxidase subunit VIc
Occurring in:
  1. Cytochrome c oxidase subunit 6C
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02937 (Cytochrome c oxidase subunit VIc) in Cytochrome c oxidase subunit 6C. Showing 1 copy in chain I.

PF02297
Domain description: Cytochrome oxidase c subunit VIb
Occurring in:
  1. Cytochrome c oxidase subunit 6B1
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02297 (Cytochrome oxidase c subunit VIb) in Cytochrome c oxidase subunit 6B1. Showing 1 copy in chain H.

PF02046
Domain description: Cytochrome c oxidase subunit VIa
Occurring in:
  1. Cytochrome c oxidase subunit 6A2, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02046 (Cytochrome c oxidase subunit VIa) in Cytochrome c oxidase subunit 6A2, mitochondrial. Showing 1 copy in chain G.

PF01215
Domain description: Cytochrome c oxidase subunit Vb
Occurring in:
  1. Cytochrome c oxidase subunit 5B, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF01215 (Cytochrome c oxidase subunit Vb) in Cytochrome c oxidase subunit 5B, mitochondrial. Showing 1 copy in chain F.

PF02284
Domain description: Cytochrome c oxidase subunit Va
Occurring in:
  1. Cytochrome c oxidase subunit 5A, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02284 (Cytochrome c oxidase subunit Va) in Cytochrome c oxidase subunit 5A, mitochondrial. Showing 1 copy in chain E.

PF02936
Domain description: Cytochrome c oxidase subunit IV
Occurring in:
  1. Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02936 (Cytochrome c oxidase subunit IV) in Cytochrome c oxidase subunit 4 isoform 1, mitochondrial. Showing 1 copy in chain D.

PF00510
Domain description: Cytochrome c oxidase subunit III
Occurring in:
  1. Cytochrome c oxidase subunit 3
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF00510 (Cytochrome c oxidase subunit III) in Cytochrome c oxidase subunit 3. Showing 1 copy in chain C.

PF00116
Domain description: Cytochrome C oxidase subunit II, periplasmic domain
Occurring in:
  1. Cytochrome c oxidase subunit 2
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF00116 (Cytochrome C oxidase subunit II, periplasmic domain) in Cytochrome c oxidase subunit 2. Showing 1 copy in chain B.

PF02790
Domain description: Cytochrome C oxidase subunit II, transmembrane domain
Occurring in:
  1. Cytochrome c oxidase subunit 2
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF02790 (Cytochrome C oxidase subunit II, transmembrane domain) in Cytochrome c oxidase subunit 2. Showing 1 copy in chain B.

PF00115
Domain description: Cytochrome C and Quinol oxidase polypeptide I
Occurring in:
  1. Cytochrome c oxidase subunit 1
The deposited structure of PDB entry 5wau contains 2 copies of Pfam domain PF00115 (Cytochrome C and Quinol oxidase polypeptide I) in Cytochrome c oxidase subunit 1. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR000883
Domain description: Cytochrome c oxidase subunit I
Occurring in:
  1. Cytochrome c oxidase subunit 1
IPR003213
Domain description: Cytochrome c oxidase, subunit VIb
Occurring in:
  1. Cytochrome c oxidase subunit 6B1
IPR001349
Domain description: Cytochrome c oxidase, subunit VIa
Occurring in:
  1. Cytochrome c oxidase subunit 6A2, mitochondrial
IPR002124
Domain description: Cytochrome c oxidase, subunit Vb
Occurring in:
  1. Cytochrome c oxidase subunit 5B, mitochondrial
IPR013288
Domain description: Cytochrome c oxidase subunit IV
Occurring in:
  1. Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
IPR008433
Domain description: Cytochrome C oxidase, subunit VIIB
Occurring in:
  1. Cytochrome c oxidase subunit 7B, mitochondrial
IPR003204
Domain description: Cytochrome c oxidase, subunit Va/VI
Occurring in:
  1. Cytochrome c oxidase subunit 5A, mitochondrial
IPR004203
Domain description: Cytochrome c oxidase subunit IV family
Occurring in:
  1. Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
IPR036548
Domain description: Cytochrome c oxidase, subunit 8 superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 8B, mitochondrial
IPR036636
Domain description: Cytochrome c oxidase subunit VIIc superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 7C, mitochondrial
IPR004202
Domain description: Cytochrome c oxidase subunit VIIc
Occurring in:
  1. Cytochrome c oxidase subunit 7C, mitochondrial
IPR023272
Domain description: Cytochrome C oxidase, subunit VIIB domain superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 7B, mitochondrial
IPR036539
Domain description: Cytochrome c oxidase, subunit VIIa superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 7A1, mitochondrial
IPR003177
Domain description: Cytochrome c oxidase subunit VIIa, metazoa
Occurring in:
  1. Cytochrome c oxidase subunit 7A1, mitochondrial
IPR037169
Domain description: Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 6C
IPR036549
Domain description: Cytochrome c oxidase, subunit VIb superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 6B1
IPR036418
Domain description: Cytochrome c oxidase, subunit VIa superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 6A2, mitochondrial
IPR036545
Domain description: Cytochrome c oxidase, subunit Va/VI superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 5A, mitochondrial
IPR036639
Domain description: Cytochrome c oxidase subunit IV superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
IPR000298
Domain description: Cytochrome c oxidase subunit III-like
Occurring in:
  1. Cytochrome c oxidase subunit 3
IPR002429
Domain description: Cytochrome c oxidase subunit II-like C-terminal
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR008972
Domain description: Cupredoxin
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR036257
Domain description: Cytochrome C oxidase subunit II, transmembrane domain superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR011759
Domain description: Cytochrome C oxidase subunit II, transmembrane domain
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR036927
Domain description: Cytochrome c oxidase-like, subunit I superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 1
IPR003205
Domain description: Cytochrome c oxidase, subunit 8
Occurring in:
  1. Cytochrome c oxidase subunit 8B, mitochondrial
IPR039297
Domain description: Cytochrome c oxidase subunit VII
Occurring in:
  1. Cytochrome c oxidase subunit 7A1, mitochondrial
IPR034884
Domain description: Mitochondrial cytochrome c oxidase subunit VIc/VIIs
Occurring in:
  1. Cytochrome c oxidase subunit 6C
IPR004204
Domain description: Cytochrome c oxidase subunit 7e/7s
Occurring in:
  1. Cytochrome c oxidase subunit 6C
IPR018507
Domain description: Cytochrome c oxidase, subunit VIa, conserved site
Occurring in:
  1. Cytochrome c oxidase subunit 6A2, mitochondrial
IPR036972
Domain description: Cytochrome c oxidase, subunit Vb superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 5B, mitochondrial
IPR013833
Domain description: Cytochrome c oxidase, subunit III, 4-helical bundle
Occurring in:
  1. Cytochrome c oxidase subunit 3
IPR033945
Domain description: Cytochrome c oxidase subunit III domain
Occurring in:
  1. Cytochrome c oxidase subunit 3
IPR024791
Domain description: Cytochrome c oxidase subunit III
Occurring in:
  1. Cytochrome c oxidase subunit 3
IPR035973
Domain description: Cytochrome c oxidase subunit III-like superfamily
Occurring in:
  1. Cytochrome c oxidase subunit 3
IPR001505
Domain description: Copper centre Cu(A)
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR034210
Domain description: Cytochrome c oxidase subunit 2, C-terminal
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR014222
Domain description: Cytochrome c oxidase, subunit II
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR045187
Domain description: Cytochrome c/quinol oxidase subunit II
Occurring in:
  1. Cytochrome c oxidase subunit 2
IPR023615
Domain description: Cytochrome c oxidase, subunit I, copper-binding site
Occurring in:
  1. Cytochrome c oxidase subunit 1
IPR033944
Domain description: Cytochrome c oxidase subunit I domain
Occurring in:
  1. Cytochrome c oxidase subunit 1
IPR023616
Domain description: Cytochrome c oxidase-like, subunit I domain
Occurring in:
  1. Cytochrome c oxidase subunit 1

Structure domains

CATH CATH domains
4.10.81.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Cytochrome C Oxidase; Chain M
Homology: Cytochrome c oxidase, subunit 8
Occurring in:
  1. Cytochrome c oxidase subunit 8B, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 4.10.81.10 (Cytochrome C Oxidase; Chain M) in Cytochrome c oxidase subunit 8B, mitochondrial. Showing 1 copy in chain M.
4.10.49.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Cytochrome C Oxidase; Chain L
Homology: Cytochrome c oxidase subunit VIIc
Occurring in:
  1. Cytochrome c oxidase subunit 7C, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 4.10.49.10 (Cytochrome C Oxidase; Chain L) in Cytochrome c oxidase subunit 7C, mitochondrial. Showing 1 copy in chain L.
4.10.51.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Cytochrome C Oxidase; Chain K
Homology: Cytochrome C Oxidase, chain K
Occurring in:
  1. Cytochrome c oxidase subunit 7B, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 4.10.51.10 (Cytochrome C Oxidase; Chain K) in Cytochrome c oxidase subunit 7B, mitochondrial. Showing 1 copy in chain K.
4.10.91.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Cytochrome C Oxidase; Chain J
Homology: Cytochrome c oxidase, subunit VIIa
Occurring in:
  1. Cytochrome c oxidase subunit 7A1, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 4.10.91.10 (Cytochrome C Oxidase; Chain J) in Cytochrome c oxidase subunit 7A1, mitochondrial. Showing 1 copy in chain J.
4.10.93.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Cytochrome C Oxidase; Chain I
Homology: Mitochondrial cytochrome c oxidase subunit VIc/VIIs
Occurring in:
  1. Cytochrome c oxidase subunit 6C
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 4.10.93.10 (Cytochrome C Oxidase; Chain I) in Cytochrome c oxidase subunit 6C. Showing 1 copy in chain I.
1.10.10.140
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Arc Repressor Mutant, subunit A
Homology: Cytochrome c oxidase, subunit VIb
Occurring in:
  1. Cytochrome c oxidase subunit 6B1
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.10.10.140 (Arc Repressor Mutant, subunit A) in Cytochrome c oxidase subunit 6B1. Showing 1 copy in chain H.
4.10.95.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Cytochrome C Oxidase; Chain G
Homology: Cytochrome c oxidase, subunit VIa
Occurring in:
  1. Cytochrome c oxidase subunit 6A2, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 4.10.95.10 (Cytochrome C Oxidase; Chain G) in Cytochrome c oxidase subunit 6A2, mitochondrial. Showing 1 copy in chain G.
2.60.11.10
Class: Mainly Beta
Architecture: Sandwich
Topology: Cytochrome C Oxidase; Chain F
Homology: Cytochrome c oxidase, subunit Vb
Occurring in:
  1. Cytochrome c oxidase subunit 5B, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 2.60.11.10 (Cytochrome C Oxidase; Chain F) in Cytochrome c oxidase subunit 5B, mitochondrial. Showing 1 copy in chain F.
1.25.40.40
Class: Mainly Alpha
Architecture: Alpha Horseshoe
Topology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homology: Cytochrome c oxidase, subunit Va/VI
Occurring in:
  1. Cytochrome c oxidase subunit 5A, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.25.40.40 (Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat) in Cytochrome c oxidase subunit 5A, mitochondrial. Showing 1 copy in chain E.
1.10.442.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Cytochrome C Oxidase; Chain D
Homology: Cytochrome c oxidase subunit IV
Occurring in:
  1. Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.10.442.10 (Cytochrome C Oxidase; Chain D) in Cytochrome c oxidase subunit 4 isoform 1, mitochondrial. Showing 1 copy in chain D.
1.20.120.80
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Four Helix Bundle (Hemerythrin (Met), subunit A)
Homology: Cytochrome c oxidase, subunit III, four-helix bundle
Occurring in:
  1. Cytochrome c oxidase subunit 3
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.20.120.80 (Four Helix Bundle (Hemerythrin (Met), subunit A)) in Cytochrome c oxidase subunit 3. Showing 1 copy in chain C.
1.10.287.70
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: Helix Hairpins
Occurring in:
  1. Cytochrome c oxidase subunit 3
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.10.287.70 (Helix Hairpins) in Cytochrome c oxidase subunit 3. Showing 1 copy in chain C.
2.60.40.420
Class: Mainly Beta
Architecture: Sandwich
Topology: Immunoglobulin-like
Homology: Cupredoxins - blue copper proteins
Occurring in:
  1. Cytochrome c oxidase subunit 2
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 2.60.40.420 (Immunoglobulin-like) in Cytochrome c oxidase subunit 2. Showing 1 copy in chain B.
1.10.287.90
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: Helix Hairpins
Occurring in:
  1. Cytochrome c oxidase subunit 2
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.10.287.90 (Helix Hairpins) in Cytochrome c oxidase subunit 2. Showing 1 copy in chain B.
1.20.210.10
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Cytochrome C Oxidase; Chain A
Homology: Cytochrome c oxidase-like, subunit I domain
Occurring in:
  1. Cytochrome c oxidase subunit 1
The deposited structure of PDB entry 5wau contains 2 copies of CATH domain 1.20.210.10 (Cytochrome C Oxidase; Chain A) in Cytochrome c oxidase subunit 1. Showing 1 copy in chain A.

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