5XTD: Cryo-EM structure of human respiratory complex I

PDB ID: 5XTDDownload
MMDB ID: 154184
PDB Deposition Date: 2017/6/19
Updated in MMDB: 2017/12
Experimental Method:
electron microscopy
Resolution: 3.7  Å
Source Organism:
Similar Structures:
Biological Unit for 5XTD: 45-meric; determined by author
Molecular Components in 5XTD
Label Count Molecule
Proteins (45 molecules)
1
Nadh Dehydrogenase [ubiquinone] Flavoprotein 1, Mitochondrial
(Gene symbol: NDUFV1)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 8, Mitochondrial
(Gene symbol: NDUFS8)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 7, Mitochondrial
(Gene symbol: NDUFS7)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 6
(Gene symbol: NDUFA6)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 2
(Gene symbol: NDUFA2)
Molecule annotation
2
Acyl Carrier Protein, Mitochondrial
(Gene symbol: NDUFAB1)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 5
(Gene symbol: NDUFA5)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 7
(Gene symbol: NDUFA7)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 9, Mitochondrial
(Gene symbol: NDUFA9)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Flavoprotein 3, Mitochondrial
(Gene symbol: NDUFV3)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 4, Mitochondrial
(Gene symbol: NDUFS4)
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase 75 KDA Subunit, Mitochondrial
(Gene symbol: NDUFS1)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 12
(Gene symbol: NDUFA12)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Flavoprotein 2, Mitochondrial
(Gene symbol: NDUFV2)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 3, Mitochondrial
(Gene symbol: NDUFS3)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 2, Mitochondrial
(Gene symbol: NDUFS2)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 1
(Gene symbol: NDUFA1)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 6, Mitochondrial
(Gene symbol: NDUFS6)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 3
(Gene symbol: NDUFA3)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 11
(Gene symbol: NDUFA11)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 13
(Gene symbol: NDUFA13)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 2, Mitochondrial
(Gene symbol: NDUFB2)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 3
(Gene symbol: NDUFB3)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 5, Mitochondrial
(Gene symbol: NDUFB5)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 6
(Gene symbol: NDUFB6)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 8, Mitochondrial
(Gene symbol: NDUFB8)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 10
(Gene symbol: NDUFB10)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 11, Mitochondrial
(Gene symbol: NDUFB11)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Subunit C1, Mitochondrial
(Gene symbol: NDUFC1)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Subunit C2
(Gene symbol: NDUFC2)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 5
(Gene symbol: NDUFS5)
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 2
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 3
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 4L
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 5
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 6
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 1
(Gene symbol: NDUFB1)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 4
(Gene symbol: NDUFB4)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 9
(Gene symbol: NDUFB9)
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 4
Molecule annotation
1
Nadh-ubiquinone Oxidoreductase Chain 1
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 8
(Gene symbol: NDUFA8)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 7
(Gene symbol: NDUFB7)
Molecule annotation
1
Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 10, Mitochondrial
(Gene symbol: NDUFA10)
Molecule annotation
Chemicals and Non-standard biopolymers (30 molecules)
1
6
IRON/SULFUR CLUSTER (Link to PubChem not yet available)IRON/SULFUR CLUSTER
2
1
FLAVIN MONONUCLEOTIDE (Link to PubChem not yet available)FLAVIN MONONUCLEOTIDE
3
9
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL (Link to PubChem not yet available)(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
4
2
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (Link to PubChem not yet available)S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
5
1
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (Link to PubChem not yet available)NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
6
2
FE2/S2 (INORGANIC) CLUSTER (Link to PubChem not yet available)FE2/S2 (INORGANIC) CLUSTER
7
5
CARDIOLIPIN (Link to PubChem not yet available)CARDIOLIPIN
8
4
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (Link to PubChem not yet available)1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
* 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