› 8c2s

Electron Microscopy
3.9Å resolution

Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 1).

Released:
DOI: 10.2210/pdb8c2s/pdb
PDB entry 8c2s coloured by chain, front view.
PDB entry 8c2s coloured by chain, side view.
PDB entry 8c2s coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4-/- mouse.
Yin Z, Agip AA, Bridges HR, Hirst J
EMBO J (2024)
PMID: 38177503
Related structures: EMD-16398

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 43-mer (preferred)
PDBe Complex ID:
PDB-CPX-236902 (preferred)
Entry contents:
42 distinct polypeptide molecules
Macromolecules (42 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
Length: 115 amino acids
Theoretical weight: 13.25 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: 52.72 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: 245 amino acids
Theoretical weight: 27.08 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D6J6 (Residues: 1-245; Coverage: 99%)
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: 36.11 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-ubiquinone oxidoreductase chain 6 Chain: J
Molecule details ›
Chain: J
Length: 171 amino acids
Theoretical weight: 18.54 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03925 (Residues: 1-171; Coverage: 99%)
Gene names: Mtnd6, Nd6, mt-Nd6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH-ubiquinone oxidoreductase chain 4L Chain: K
Molecule details ›
Chain: K
Length: 98 amino acids
Theoretical weight: 10.64 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03903 (Residues: 1-98; Coverage: 100%)
Gene names: Mtnd4l, Nd4l, mt-Nd4l
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5 Chain: L
Molecule details ›
Chain: L
Length: 606 amino acids
Theoretical weight: 68.42 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03921 (Residues: 1-606; Coverage: 100%)
Gene names: Mtnd5, Nd5, mt-Nd5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4 Chain: M
Molecule details ›
Chain: M
Length: 459 amino acids
Theoretical weight: 51.94 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03911 (Residues: 1-459; Coverage: 100%)
Gene names: Mtnd4, Nd4, mt-Nd4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 2 Chain: N
Molecule details ›
Chain: N
Length: 345 amino acids
Theoretical weight: 38.8 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P03893 (Residues: 1-345; Coverage: 100%)
Gene names: Nd2, mt-Nd2
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: O
Molecule details ›
Chain: O
Length: 355 amino acids
Theoretical weight: 40.66 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q99LC3 (Residues: 1-355; Coverage: 100%)
Gene name: Ndufa10
Sequence domains: Deoxynucleoside kinase
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 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 Chains: T, U
Molecule details ›
Chains: T, U
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 11 Chain: Y
Molecule details ›
Chain: Y
Length: 143 amino acids
Theoretical weight: 15.13 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: G5E814 (Residues: 1-143; Coverage: 100%)
Gene name: Ndufa11
Sequence domains: Tim17/Tim22/Tim23/Pmp24 family
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 subunit C1, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 76 amino acids
Theoretical weight: 8.64 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQY9 (Residues: 1-76; Coverage: 100%)
Gene name: Ndufc1
Sequence domains: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: d
Molecule details ›
Chain: d
Length: 120 amino acids
Theoretical weight: 14.19 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQ54 (Residues: 1-120; Coverage: 100%)
Gene name: Ndufc2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: e
Molecule details ›
Chain: e
Length: 106 amino acids
Theoretical weight: 12.68 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q99LY9 (Residues: 1-106; Coverage: 100%)
Gene name: Ndufs5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: f
Molecule details ›
Chain: f
Length: 57 amino acids
Theoretical weight: 6.97 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P0DN34 (Residues: 1-57; Coverage: 100%)
Gene name: Ndufb1
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: g
Molecule details ›
Chain: g
Length: 151 amino acids
Theoretical weight: 17.46 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: O09111 (Residues: 1-151; Coverage: 100%)
Gene names: Ndufb11, Np15
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: h
Molecule details ›
Chain: h
Length: 189 amino acids
Theoretical weight: 21.74 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQH3 (Residues: 1-189; Coverage: 100%)
Gene name: Ndufb5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: i
Molecule details ›
Chain: i
Length: 127 amino acids
Theoretical weight: 15.45 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q3UIU2 (Residues: 2-128; Coverage: 99%)
Gene names: Gm137, Ndufb6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chain: j
Molecule details ›
Chain: j
Length: 105 amino acids
Theoretical weight: 11.98 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CPU2 (Residues: 1-105; Coverage: 100%)
Gene name: Ndufb2
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: k
Molecule details ›
Chain: k
Length: 104 amino acids
Theoretical weight: 11.71 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQZ6 (Residues: 1-104; Coverage: 100%)
Gene name: Ndufb3
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: l
Molecule details ›
Chain: l
Length: 186 amino acids
Theoretical weight: 21.9 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D6J5 (Residues: 1-186; Coverage: 100%)
Gene name: Ndufb8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: m
Molecule details ›
Chain: m
Length: 129 amino acids
Theoretical weight: 15.11 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQC7 (Residues: 1-129; Coverage: 100%)
Gene name: Ndufb4
Sequence domains: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: n
Molecule details ›
Chain: n
Length: 179 amino acids
Theoretical weight: 22.02 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQJ8 (Residues: 1-179; Coverage: 100%)
Gene name: Ndufb9
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: o
Molecule details ›
Chain: o
Length: 137 amino acids
Theoretical weight: 16.36 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CR61 (Residues: 1-137; Coverage: 100%)
Gene name: Ndufb7
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: p
Molecule details ›
Chain: p
Length: 176 amino acids
Theoretical weight: 21.05 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DCS9 (Residues: 1-176; Coverage: 100%)
Gene name: Ndufb10
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
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

11 bound ligands:
Ligand SF4 6 x SF4
Ligand PC1 2 x PC1
Ligand FES 2 x FES
Ligand FMN 1 x FMN
Ligand 3PE 7 x 3PE
Ligand CDL 6 x CDL
Ligand LMT 2 x LMT
Ligand GTP 1 x GTP
Ligand NAP 1 x NAP
Ligand ZN 1 x ZN
Ligand EHZ 2 x EHZ
3 modified residues:
Ligand FME 7 x FME
Ligand 2MR 1 x 2MR
Ligand SAC 1 x SAC

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-16398

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