› 5xtc

Electron Microscopy
3.7Å resolution

Cryo-EM structure of human respiratory complex I transmembrane arm

Released:
DOI: 10.2210/pdb5xtc/pdb
PDB entry 5xtc coloured by chain, front view.
PDB entry 5xtc coloured by chain, side view.
PDB entry 5xtc 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-6772

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 29-mer (preferred)
PDBe Complex ID:
PDB-CPX-127009 (preferred)
Entry contents:
29 distinct polypeptide molecules
Macromolecules (29 distinct):
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 46 amino acids
Theoretical weight: 5.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75306 (Residues: 34-79; Coverage: 10%)
Gene name: NDUFS2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: S
Molecule details ›
Chain: S
Length: 70 amino acids
Theoretical weight: 8.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15239 (Residues: 1-70; Coverage: 100%)
Gene name: NDUFA1
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: U
Molecule details ›
Chain: U
Length: 83 amino acids
Theoretical weight: 9.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95167 (Residues: 2-84; Coverage: 99%)
Gene name: NDUFA3
Sequence domains: NADH dehydrogenase 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q86Y39 (Residues: 2-141; Coverage: 99%)
Gene name: NDUFA11
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
Length: 116 amino acids
Theoretical weight: 13.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0J0 (Residues: 29-144; Coverage: 81%)
Gene names: CDA016, CGI-39, GRIM19, NDUFA13
Sequence domains: GRIM-19 protein
Acyl carrier protein, mitochondrial Chain: X
Molecule details ›
Chain: X
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 beta subcomplex subunit 2, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 59 amino acids
Theoretical weight: 7.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95178 (Residues: 39-97; Coverage: 56%)
Gene name: NDUFB2
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: Z
Molecule details ›
Chain: Z
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43676 (Residues: 10-89; Coverage: 82%)
Gene name: NDUFB3
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 138 amino acids
Theoretical weight: 16.57 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43674 (Residues: 52-189; Coverage: 73%)
Gene name: NDUFB5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: b
Molecule details ›
Chain: b
Length: 128 amino acids
Theoretical weight: 15.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95139 (Residues: 1-128; Coverage: 100%)
Gene name: NDUFB6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 153 amino acids
Theoretical weight: 18.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95169 (Residues: 34-186; Coverage: 82%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: d
Molecule details ›
Chain: d
Length: 171 amino acids
Theoretical weight: 20.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O96000 (Residues: 1-171; Coverage: 99%)
Gene name: NDUFB10
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: e
Molecule details ›
Chain: e
Length: 97 amino acids
Theoretical weight: 11.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NX14 (Residues: 54-150; Coverage: 63%)
Gene names: NDUFB11, UNQ111/PRO1064
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 47 amino acids
Theoretical weight: 5.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43677 (Residues: 28-74; Coverage: 62%)
Gene name: NDUFC1
Sequence domains: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: g
Molecule details ›
Chain: g
Length: 119 amino acids
Theoretical weight: 14.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95298 (Residues: 1-119; Coverage: 100%)
Gene names: HLC1, NDUFC2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: h
Molecule details ›
Chain: h
Length: 104 amino acids
Theoretical weight: 12.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43920 (Residues: 2-105; Coverage: 98%)
Gene name: NDUFS5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH-ubiquinone oxidoreductase chain 2 Chain: i
Molecule details ›
Chain: i
Length: 347 amino acids
Theoretical weight: 39.01 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03891 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH-ubiquinone oxidoreductase chain 3 Chain: j
Molecule details ›
Chain: j
Length: 115 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03897 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
Structure domains: NADH:ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4L Chain: k
Molecule details ›
Chain: k
Length: 97 amino acids
Theoretical weight: 10.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03901 (Residues: 1-97; Coverage: 99%)
Gene names: MT-ND4L, MTND4L, NADH4L, ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
Structure domains: Helix Hairpins
NADH-ubiquinone oxidoreductase chain 5 Chain: l
Molecule details ›
Chain: l
Length: 603 amino acids
Theoretical weight: 67.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03915 (Residues: 1-603; Coverage: 100%)
Gene names: MT-ND5, MTND5, NADH5, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 6 Chain: m
Molecule details ›
Chain: m
Length: 174 amino acids
Theoretical weight: 18.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03923 (Residues: 1-174; Coverage: 100%)
Gene names: MT-ND6, MTND6, NADH6, ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: n
Molecule details ›
Chain: n
Length: 56 amino acids
Theoretical weight: 6.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75438 (Residues: 3-58; Coverage: 97%)
Gene name: NDUFB1
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: o
Molecule details ›
Chain: o
Length: 128 amino acids
Theoretical weight: 15.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95168 (Residues: 2-129; Coverage: 99%)
Gene name: NDUFB4
Sequence domains: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: p
Molecule details ›
Chain: p
Length: 172 amino acids
Theoretical weight: 21.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y6M9 (Residues: 8-179; Coverage: 96%)
Gene names: LYRM3, NDUFB9, UQOR22
Sequence domains: Complex 1 protein (LYR family)
NADH-ubiquinone oxidoreductase chain 4 Chain: r
Molecule details ›
Chain: r
Length: 459 amino acids
Theoretical weight: 51.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03905 (Residues: 1-459; Coverage: 100%)
Gene names: MT-ND4, MTND4, NADH4, ND4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: s
Molecule details ›
Chain: s
Length: 318 amino acids
Theoretical weight: 35.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03886 (Residues: 1-318; Coverage: 100%)
Gene names: MT-ND1, MTND1, NADH1, ND1
Sequence domains: NADH dehydrogenase
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: u
Molecule details ›
Chain: u
Length: 169 amino acids
Theoretical weight: 19.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P51970 (Residues: 4-172; Coverage: 98%)
Gene name: NDUFA8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: v
Molecule details ›
Chain: v
Length: 122 amino acids
Theoretical weight: 15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P17568 (Residues: 3-124; Coverage: 89%)
Gene name: NDUFB7
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: w
Molecule details ›
Chain: w
Length: 320 amino acids
Theoretical weight: 37.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95299 (Residues: 36-355; Coverage: 90%)
Gene name: NDUFA10
Sequence domains: Deoxynucleoside kinase

Ligands and Environments

4 bound ligands:
Ligand PLX 9 x PLX
Ligand CDL 5 x CDL
Ligand PEE 4 x PEE
Ligand 8Q1 1 x 8Q1
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-6772

Quick links

Citations

62 review citations

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

14 mentions without citation

Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.
Grba et al. (2020)
13 more