› 8xnw

Electron Microscopy
3.6Å resolution

Respiratory complex Peripheral Arm of CI, close form B, focus-refined map of type II, Wild type mouse under Cold Acclimation

Released:
DOI: 10.2210/pdb8xnw/pdb
PDB entry 8xnw coloured by chain, front view.
PDB entry 8xnw coloured by chain, side view.
PDB entry 8xnw coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural basis of respiratory complex adaptation to cold temperatures.
Shin YC, Latorre-Muro P, Djurabekova A, Zdorevskyi O, Bennett CF, Burger N, Song K, Xu C, Paulo JA, Gygi SP, Sharma V, Liao M, Puigserver P
Cell (2024)
PMID: 39395414
Related structures: EMD-38517

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-271665 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
Length: 115 amino acids
Theoretical weight: 13.22 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03899 (Residues: 1-115; Coverage: 100%)
Gene names: Nd3, mt-Nd3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 224 amino acids
Theoretical weight: 24.72 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DC70 (Residues: 1-224; Coverage: 100%)
Gene name: Ndufs7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 263 amino acids
Theoretical weight: 30.19 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DCT2 (Residues: 1-263; Coverage: 100%)
Gene name: Ndufs3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 463 amino acids
Theoretical weight: 52.69 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q91WD5 (Residues: 1-463; Coverage: 100%)
Gene name: Ndufs2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 248 amino acids
Theoretical weight: 27.32 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D6J6 (Residues: 1-248; Coverage: 100%)
Gene name: Ndufv2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 464 amino acids
Theoretical weight: 50.9 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q91YT0 (Residues: 1-464; Coverage: 100%)
Gene name: Ndufv1
Sequence domains:
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 727 amino acids
Theoretical weight: 79.87 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q91VD9 (Residues: 1-727; Coverage: 100%)
Gene name: Ndufs1
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: H
Molecule details ›
Chain: H
Length: 318 amino acids
Theoretical weight: 36.08 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03888 (Residues: 1-318; Coverage: 100%)
Gene names: Mtnd1, Nd1, mt-Nd1
Sequence domains: NADH dehydrogenase
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 212 amino acids
Theoretical weight: 24.07 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8K3J1 (Residues: 1-212; Coverage: 100%)
Gene name: Ndufs8
Sequence domains: 4Fe-4S dicluster domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 377 amino acids
Theoretical weight: 42.59 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DC69 (Residues: 1-377; Coverage: 100%)
Gene name: Ndufa9
Sequence domains: NmrA-like family
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 175 amino acids
Theoretical weight: 19.81 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CXZ1 (Residues: 1-175; Coverage: 100%)
Gene name: Ndufs4
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 116 amino acids
Theoretical weight: 13.04 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P52503 (Residues: 1-116; Coverage: 100%)
Gene names: Ip13, Ndufs6
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: S
Molecule details ›
Chain: S
Length: 99 amino acids
Theoretical weight: 10.93 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQ75 (Residues: 1-99; Coverage: 100%)
Gene name: Ndufa2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Acyl carrier protein, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 156 amino acids
Theoretical weight: 17.39 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CR21 (Residues: 1-156; Coverage: 100%)
Gene name: Ndufab1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: V
Molecule details ›
Chain: V
Length: 116 amino acids
Theoretical weight: 13.38 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CPP6 (Residues: 1-116; Coverage: 100%)
Gene name: Ndufa5
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: W
Molecule details ›
Chain: W
Length: 131 amino acids
Theoretical weight: 15.31 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQZ5 (Residues: 1-131; Coverage: 100%)
Gene name: Ndufa6
Sequence domains: Complex1_LYR-like
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: X
Molecule details ›
Chain: X
Length: 172 amino acids
Theoretical weight: 20.03 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DCJ5 (Residues: 1-172; Coverage: 100%)
Gene name: Ndufa8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: Z
Molecule details ›
Chain: Z
Length: 144 amino acids
Theoretical weight: 16.88 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9ERS2 (Residues: 1-144; Coverage: 100%)
Gene names: Grim19, Ndufa13
Sequence domains: GRIM-19 protein
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 70 amino acids
Theoretical weight: 8.15 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: O35683 (Residues: 1-70; Coverage: 100%)
Gene name: Ndufa1
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: b
Molecule details ›
Chain: b
Length: 84 amino acids
Theoretical weight: 9.34 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQ91 (Residues: 1-84; Coverage: 100%)
Gene name: Ndufa3
Sequence domains: NADH dehydrogenase 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: q
Molecule details ›
Chain: q
Length: 145 amino acids
Theoretical weight: 17.11 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q7TMF3 (Residues: 1-145; Coverage: 100%)
Gene name: Ndufa12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: r
Molecule details ›
Chain: r
Length: 113 amino acids
Theoretical weight: 12.6 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9Z1P6 (Residues: 1-113; Coverage: 100%)
Gene name: Ndufa7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: s
Molecule details ›
Chain: s
Length: 104 amino acids
Theoretical weight: 11.83 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8BK30 (Residues: 1-104; Coverage: 100%)
Gene name: Ndufv3
Sequence domains: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

Ligands and Environments

10 bound ligands:
Ligand SF4 6 x SF4
Ligand UQ9 2 x UQ9
Ligand PC1 1 x PC1
Ligand FES 2 x FES
Ligand FMN 1 x FMN
Ligand 3PE 1 x 3PE
Ligand NDP 1 x NDP
Ligand ZN 1 x ZN
Ligand EHZ 1 x EHZ
Ligand CDL 1 x CDL
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-38517

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