SMTL ID : 8ca4.1

Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2 N-domain).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 9 residues within 4Å: Chain A: C.134, T.136, P.138, C.139, C.175, L.176, G.177, A.178, C.179 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.134, A:C.139, A:C.175, A:C.179 FES.6: 9 residues within 4Å: Chain C: R.62, F.63, C.64, Y.65, G.73, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.64, C:C.75, C:C.78, C:C.92

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 13 residues within 4Å: Chain B: I.205, P.223, C.379, G.380, Q.381, C.382, C.385, R.386, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.379, B:C.382, B:C.385, B:C.425 SF4.4: 11 residues within 4Å: Chain C: H.124, P.125, D.127, C.128, C.131, Q.133, C.137, L.139, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.124, C:C.128, C:C.131, C:C.137 SF4.5: 13 residues within 4Å: Chain C: M.173, C.176, I.177, Q.178, C.179, T.180, C.182, V.206, C.226, P.227, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.176, C:C.179, C:C.182, C:C.226

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 20 residues within 4Å: Chain B: G.87, R.88, G.89, G.90, A.91, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.204, B:Y.204, B:E.208, B:A.426, B:L.427 Hydrogen bonds: B:R.88, B:G.89, B:G.90, B:N.116, B:G.120, B:G.207, B:E.209, B:V.242, B:N.244, B:N.244 Salt bridges: B:K.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4 -/- mouse. Embo J. (2024)

Release Date

2023-12-20

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: A
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: B
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: D
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
S

E
s

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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