› 5xtb

Electron Microscopy
3.4Å resolution

Cryo-EM structure of human respiratory complex I matrix arm

Released:
DOI: 10.2210/pdb5xtb/pdb
PDB entry 5xtb coloured by chain, front view.
PDB entry 5xtb coloured by chain, side view.
PDB entry 5xtb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.
Guo R, Zong S, Wu M, Gu J, Yang M
Cell 170 1247-1257.e12 (2017)
PMID: 28844695
Related structures: EMD-6771

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-126164 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 431 amino acids
Theoretical weight: 47.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49821 (Residues: 27-457; Coverage: 93%)
Gene names: NDUFV1, UQOR1
Sequence domains:
Structure domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 176 amino acids
Theoretical weight: 20.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00217 (Residues: 35-210; Coverage: 84%)
Gene name: NDUFS8
Sequence domains: 4Fe-4S dicluster domain
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 156 amino acids
Theoretical weight: 17.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75251 (Residues: 58-213; Coverage: 73%)
Gene name: NDUFS7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
Structure domains: Rossmann fold
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: E
Molecule details ›
Chain: E
Length: 113 amino acids
Theoretical weight: 13.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56556 (Residues: 16-128; Coverage: 88%)
Gene names: LYRM6, NADHB14, NDUFA6
Sequence domains: Complex1_LYR-like
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: F
Molecule details ›
Chain: F
Length: 83 amino acids
Theoretical weight: 9.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43678 (Residues: 14-96; Coverage: 84%)
Gene name: NDUFA2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Structure domains: Glutaredoxin
Acyl carrier protein, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 85 amino acids
Theoretical weight: 9.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14561 (Residues: 72-156; Coverage: 55%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: H
Molecule details ›
Chain: H
Length: 112 amino acids
Theoretical weight: 13.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16718 (Residues: 5-116; Coverage: 97%)
Gene name: NDUFA5
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: I
Molecule details ›
Chain: I
Length: 110 amino acids
Theoretical weight: 12.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95182 (Residues: 4-113; Coverage: 97%)
Gene name: NDUFA7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 337 amino acids
Theoretical weight: 38.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16795 (Residues: 40-376; Coverage: 89%)
Gene names: NDUFA9, NDUFS2L
Sequence domains: NAD dependent epimerase/dehydratase family
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: K
Molecule details ›
Chain: K
Length: 33 amino acids
Theoretical weight: 3.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56181 (Residues: 74-106; Coverage: 31%)
Gene name: NDUFV3
Sequence domains: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: L
Molecule details ›
Chain: L
Length: 118 amino acids
Theoretical weight: 13.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43181 (Residues: 58-175; Coverage: 67%)
Gene name: NDUFS4
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 687 amino acids
Theoretical weight: 75.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28331 (Residues: 30-716; Coverage: 95%)
Gene name: NDUFS1
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: N
Molecule details ›
Chain: N
Length: 143 amino acids
Theoretical weight: 16.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UI09 (Residues: 2-144; Coverage: 99%)
Gene names: DAP13, NDUFA12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: O
Molecule details ›
Chain: O
Length: 212 amino acids
Theoretical weight: 23.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19404 (Residues: 36-247; Coverage: 85%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 208 amino acids
Theoretical weight: 24.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75489 (Residues: 43-250; Coverage: 79%)
Gene name: NDUFS3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 385 amino acids
Theoretical weight: 43.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75306 (Residues: 79-463; Coverage: 83%)
Gene name: NDUFS2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
Structure domains: Cytochrome-c3 Hydrogenase, chain B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 95 amino acids
Theoretical weight: 10.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75380 (Residues: 29-123; Coverage: 77%)
Gene name: NDUFS6
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
Length: 22 amino acids
Theoretical weight: 2.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0J0 (Residues: 7-28; Coverage: 15%)
Gene names: CDA016, CGI-39, GRIM19, NDUFA13

Ligands and Environments

5 bound ligands:
Ligand SF4 6 x SF4
Ligand FMN 1 x FMN
Ligand 8Q1 1 x 8Q1
Ligand NDP 1 x NDP
Ligand FES 2 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-6771

Quick links

Citations

62 review citations

The multifaceted role of iron in renal health and disease.
van Swelm et al. (2020)
61 more

9 mentions without citation

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network.
Kahraman et al. (2020)
8 more