7DEG: Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism

PDB ID: 7DEGDownload
MMDB ID: 205188
PDB Deposition Date: 2020/11/4
Updated in MMDB: 2025/09
Experimental Method:
electron microscopy
Resolution: 3.4  Å
Source Organism:
Aquifex aeolicus VF5▼
Similar Structures:
Biological Unit for 7DEG: hexameric; determined by author
Molecular Components in 7DEG
Label Count Molecule
Proteins (6 molecules)
2
Cytochrome C Oxidase Subunit I
Molecule annotation
2
Cytochrome Oxidase Subunit IIA
Molecule annotation
2
Cytochrome Oxidase Subunit II
Molecule annotation
Chemicals and Non-standard biopolymers (18 molecules)
1
2
HEME-ASHEME-AS
2
2
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
3
2
COPPER (II) IONCOPPER (II) ION
4
2
2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
5
6
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
6
2
1,2-Distearoyl-sn-glycerophosphoethanolamine1,2-Distearoyl-sn-glycerophosphoethanolamine
7
2
DINUCLEAR COPPER IONDINUCLEAR COPPER ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303