8UGR: In-situ structure of typeX supercomplex in respiratory chain (composite)

PDB ID: 8UGRDownload
MMDB ID: 248604
PDB Deposition Date: 2023/10/6
Updated in MMDB: 2024/07
Experimental Method:
electron microscopy
Resolution: 6.5  Å
Source Organism:
Similar Structures:
Biological Unit for 8UGR: 162-meric; determined by author and by software
Molecular Components in 8UGR
Label Count Molecule
Proteins (162 molecules)
2
Nadh-ubiquinone Oxidoreductase Chain 3
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 7, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 3, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 2, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Flavoprotein 2, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Flavoprotein 1, Mitochondrial
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase 75 KDA Subunit, Mitochondrial
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase Chain 1
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 8, Mitochondrial
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase Chain 6
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase Chain 4L
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase Chain 5
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase Chain 4
Molecule annotation
2
Nadh-ubiquinone Oxidoreductase Chain 2
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 10, Mitochondrial
Molecule annotation
2
Nadh:ubiquinone Oxidoreductase Subunit A9
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 4, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 6, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 2
Molecule annotation
4
Nadh:ubiquinone Oxidoreductase Subunit AB1
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 5 Isoform X1
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 6
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 8
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 11
Molecule annotation
2
Nadh:ubiquinone Oxidoreductase Subunit A13
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 1
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 3
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Subunit C1, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Subunit C2
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 5
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 1 [sus Scrofa]
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 11, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 5, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 6
Molecule annotation
2
Nadh:ubiquinone Oxidoreductase Subunit B2
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 3
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 8, Mitochondrial
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 4
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 9
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 7
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 10
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 12
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 7
Molecule annotation
2
Nadh Dehydrogenase [ubiquinone] Flavoprotein 3, Mitochondrial
Molecule annotation
4
Cytochrome B-c1 Complex Subunit 1, Mitochondrial
Molecule annotation
4
Cytochrome B-c1 Complex Subunit 2, Mitochondrial
Molecule annotation
4
Cytochrome B
Molecule annotation
4
Cytochrome C1
Molecule annotation
8
Cytochrome B-c1 Complex Subunit Rieske, Mitochondrial
Molecule annotation
4
Cytochrome B-c1 Complex Subunit 7
Molecule annotation
4
Cytochrome B-c1 Complex Subunit 8
Molecule annotation
4
Cytochrome B-c1 Complex Subunit 6, Mitochondrial
Molecule annotation
4
Ubiquinol-cytochrome C Reductase Complex 7.2 KDA Protein
Molecule annotation
4
Cytochrome B-c1 Complex Subunit 10
Molecule annotation
2
Cytochrome C Oxidase Subunit 1
Molecule annotation
2
Cytochrome C Oxidase Subunit 2
Molecule annotation
2
Cytochrome C Oxidase Subunit 3
Molecule annotation
2
Cytochrome C Oxidase Subunit 4
Molecule annotation
2
Cytochrome C Oxidase Subunit 5A, Mitochondrial
Molecule annotation
2
Cytochrome C Oxidase Subunit 5B, Mitochondrial
Molecule annotation
2
Cytochrome C Oxidase Subunit 6A2
Molecule annotation
2
Cytochrome C Oxidase Subunit 6B1
Molecule annotation
2
Cytochrome C Oxidase Subunit 6C
Molecule annotation
2
Cytochrome C Oxidase Subunit 7a1, Mitochondrial
Molecule annotation
2
Cytochrome C Oxidase Subunit 7B
Molecule annotation
2
Cytochrome C Oxidase Subunit 7C, Mitochondrial
Molecule annotation
2
Cytochrome C Oxidase Subunit 8
Molecule annotation
2
Cytochrome C Oxidase Subunit Ndufa4
Molecule annotation
Chemicals and Non-standard biopolymers (190 molecules)
1
36
1,2-Distearoyl-sn-glycerophosphoethanolamine1,2-Distearoyl-sn-glycerophosphoethanolamine
2
28
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3
12
IRON/SULFUR CLUSTERIRON/SULFUR CLUSTER
4
8
FE2/S2 (INORGANIC) CLUSTERFE2/S2 (INORGANIC) CLUSTER
5
2
FLAVIN MONONUCLEOTIDEFLAVIN MONONUCLEOTIDE
6
2
POTASSIUM IONPOTASSIUM ION
7
20
CARDIOLIPINCARDIOLIPIN
8
2
GUANOSINE-5'-TRIPHOSPHATEGUANOSINE-5'-TRIPHOSPHATE
9
4
MAGNESIUM IONMAGNESIUM ION
10
2
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATENADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
11
4
ZINC IONZINC ION
12
4
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
13
2
N-ACETYLMETHIONINEN-ACETYLMETHIONINE
14
2
MYRISTIC ACIDMYRISTIC ACID
15
2
N-ACETYLALANINEN-ACETYLALANINE
16
8
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
17
4
HEME CHEME C
18
30
(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
19
4
HEME-AHEME-A
20
2
COPPER (II) IONCOPPER (II) ION
21
2
SODIUM IONSODIUM ION
22
2
DINUCLEAR COPPER IONDINUCLEAR COPPER ION
23
2
(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(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
24
4
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
25
2
PHOSPHATE IONPHOSPHATE 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