› 7dgz

Electron Microscopy
3.8Å resolution

Activity optimized complex I (closed form)

Released:
DOI: 10.2210/pdb7dgz/pdb
PDB entry 7dgz coloured by chain, front view.
PDB entry 7dgz coloured by chain, side view.
PDB entry 7dgz coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex.
Jeon TJ, Lee SG, Yoo SH, Kim M, Song D, Ryu J, Park H, Kim DS, Hyun J, Kim HM, Ryu SE
Antioxid Redox Signal (2022)
PMID: 34913730
Related structures: EMD-30676

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 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-132192 (preferred)
Entry contents:
44 distinct polypeptide molecules
Macromolecules (44 distinct):
NADH-ubiquinone oxidoreductase chain 2 Chain: 2
Molecule details ›
Chain: 2
Length: 347 amino acids
Theoretical weight: 39.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03892 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH-ubiquinone oxidoreductase chain 3 Chain: 3
Molecule details ›
Chain: 3
Length: 115 amino acids
Theoretical weight: 13.06 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03898 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4 Chain: 4
NADH-ubiquinone oxidoreductase chain 4L Chain: 5
NADH-ubiquinone oxidoreductase chain 6 Chain: 7
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: 8
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: 9
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: D
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: E
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: F
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: G
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: P
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: S
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: T
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: V
Acyl carrier protein, mitochondrial Chains: M, W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chain: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: Z
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: f
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: h
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: i
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: j
NADH-ubiquinone oxidoreductase chain 1 Chain: 1
NADH-ubiquinone oxidoreductase chain 5 Chain: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: g
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: e

Ligands and Environments

8 bound ligands:
Ligand 3PE 4 x 3PE
Ligand CDL 2 x CDL
Ligand FMN 1 x FMN
Ligand SF4 6 x SF4
Ligand FES 2 x FES
Ligand ZN 1 x ZN
Ligand PC1 4 x PC1
Ligand NAP 1 x NAP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-30676

Quick links

Citations

1 review citation

An evolving view of complex II-noncanonical complexes, megacomplexes, respiration, signaling, and beyond.
Iverson et al. (2023)