SMTL ID : 8gs8.1

cryo-EM structure of the human respiratory complex II

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 34 residues within 4Å: Chain A: G.68, A.69, G.70, G.71, A.72, V.90, T.91, K.92, L.93, S.98, H.99, T.100, A.102, A.103, Q.104, G.105, Y.219, F.220, A.221, A.255, T.256, G.257, T.267, D.275, L.306, H.407, Y.408, G.439, E.440, R.451, A.454, S.456, L.457, L.460 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.102, A:L.306, A:L.306 Hydrogen bonds: A:A.69, A:A.69, A:G.71, A:A.72, A:T.91, A:K.92, A:K.92, A:L.93, A:H.99, A:T.100, A:T.100, A:G.105, A:A.221, A:G.257, A:D.275, A:D.275, A:E.440, A:E.440, A:R.451, A:A.454, A:S.456, A:S.456, A:L.457 pi-Cation interactions: A:H.407

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

FES.2: 9 residues within 4Å: Chain B: S.92, C.93, R.94, G.96, C.98, G.99, S.100, C.101, C.113 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.93, B:C.98, B:C.101, B:C.113

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

SF4.3: 12 residues within 4Å: Chain B: C.186, I.187, L.188, C.189, A.190, C.191, C.192, A.210, M.213, C.253, P.254, P.259 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.186, B:C.189, B:C.192, B:C.253

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.4: 12 residues within 4Å: Chain B: C.196, S.198, Y.206, P.209, C.243, H.244, T.245, I.246, M.247, N.248, C.249, I.263 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.196, B:C.243, B:C.249

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.5: 11 residues within 4Å: Chain B: P.197, W.201, H.244, I.246 Chain C: I.56, W.61, M.65, S.68, I.69, R.72 Chain D: Y.114 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:I.56, C:I.56, C:W.61, C:I.69, B:W.201 Hydrogen bonds: D:Y.114

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.6: 18 residues within 4Å: Chain C: H.71, R.72, G.75, I.76, L.78, S.79, H.127, T.128, G.131, H.134 Chain D: R.70, S.73, L.76, L.80, L.99, H.102, G.106, L.107 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D, Hydrophobic interactions: C:L.78, C:T.128, C:H.134, D:L.76, D:L.80, D:L.99, D:L.107 Salt bridges: C:R.72, D:R.70 pi-Stacking: C:H.71 Metal complexes: C:H.127, D:H.102

1 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.7: 17 residues within 4Å: Chain C: L.78, V.82, F.85, L.120, L.124, L.166, M.169 Chain D: L.80, A.83, Y.84, P.87, L.99, L.139, C.150, V.153, A.154, W.157 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:L.80, D:A.83, D:L.99, D:L.139, D:V.153, D:W.157, C:L.78, C:F.85, C:L.120, C:L.120, C:L.120, C:L.124, C:L.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, Z. et al., Structure of the human respiratory complex II. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-05-10

Peptides

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Succinate dehydrogenase cytochrome b560 subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial