SMTL ID : 7sss.1

Structure of the NADH-bound human COQ7:COQ9 complex by single-particle electron cryo-microscopy

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

PEV.1: 7 residues within 4Å: Chain A: F.238, Y.241, T.242, A.245 Ligands: PEV.22, PEV.37, PEV.38 Ligand excluded by PLIP PEV.2: 7 residues within 4Å: Chain A: P.214, L.217, S.218, T.221 Ligands: PEV.22, NAD.27, PEV.30 Ligand excluded by PLIP PEV.3: 3 residues within 4Å: Chain A: M.208, I.213 Ligands: PEV.37 Ligand excluded by PLIP PEV.4: 6 residues within 4Å: Chain B: F.238, Y.241, T.242 Ligands: PEV.25, PEV.26, PEV.34 Ligand excluded by PLIP PEV.5: 6 residues within 4Å: Chain B: I.213, P.214, L.217 Ligands: PEV.19, NAD.21, PEV.34 Ligand excluded by PLIP PEV.7: 13 residues within 4Å: Chain C: T.221, D.225, W.240, Y.241, R.244, A.245, A.248 Chain G: R.107, V.110, R.216, L.217 Ligands: PEV.9, PEV.16 Ligand excluded by PLIP PEV.8: 6 residues within 4Å: Chain C: F.238, Y.241, T.242, A.245 Ligands: PEV.15, PEV.20 Ligand excluded by PLIP PEV.9: 7 residues within 4Å: Chain C: P.214, S.215, L.217, S.218, T.221 Ligands: PEV.7, PEV.11 Ligand excluded by PLIP PEV.10: 4 residues within 4Å: Chain C: M.208, I.213, L.217 Ligands: PEV.20 Ligand excluded by PLIP PEV.11: 10 residues within 4Å: Chain C: P.210, H.211, P.214, S.215 Chain F: A.205, R.208, V.209, Y.212 Ligands: PEV.9, NAD.27 Ligand excluded by PLIP PEV.12: 5 residues within 4Å: Chain D: F.238, Y.241, T.242, A.245 Ligands: PEV.31 Ligand excluded by PLIP PEV.13: 7 residues within 4Å: Chain D: P.214, S.215, L.217, S.218 Ligands: PEV.17, NAD.21, PEV.36 Ligand excluded by PLIP PEV.14: 3 residues within 4Å: Chain D: M.208, L.217 Ligands: PEV.28 Ligand excluded by PLIP PEV.15: 7 residues within 4Å: Chain D: D.237, F.238 Chain E: V.110, L.111, P.113 Ligands: PEV.8, PEV.20 Ligand excluded by PLIP PEV.16: 12 residues within 4Å: Chain C: A.245, A.249, N.252, T.253, R.276 Chain E: R.65, N.116, V.117, F.120, A.121 Ligands: PEV.7, PEV.20 Ligand excluded by PLIP PEV.17: 10 residues within 4Å: Chain D: T.221, D.225, W.240, Y.241, R.244, A.245 Chain E: R.105, V.106, R.107 Ligands: PEV.13 Ligand excluded by PLIP PEV.19: 8 residues within 4Å: Chain B: P.210, P.214, S.215 Chain E: R.208, V.209, Y.212 Ligands: PEV.5, NAD.21 Ligand excluded by PLIP PEV.20: 8 residues within 4Å: Chain E: P.113, L.114, N.116, V.117 Ligands: PEV.8, PEV.10, PEV.15, PEV.16 Ligand excluded by PLIP PEV.22: 8 residues within 4Å: Chain A: T.221, W.240, Y.241, R.244, A.248 Chain F: R.107 Ligands: PEV.1, PEV.2 Ligand excluded by PLIP PEV.23: 12 residues within 4Å: Chain B: A.245, A.248, A.249, N.252, T.253, R.276 Chain F: R.65, N.116, V.117, F.120, A.121 Ligands: PEV.26 Ligand excluded by PLIP PEV.24: 6 residues within 4Å: Chain B: I.213, L.217 Chain F: V.117, L.118, A.121 Ligands: PEV.26 Ligand excluded by PLIP PEV.25: 6 residues within 4Å: Chain A: F.238 Chain F: V.110, P.113 Ligands: PEV.4, PEV.26, PEV.38 Ligand excluded by PLIP PEV.26: 8 residues within 4Å: Chain F: P.113, L.114, N.116, V.117 Ligands: PEV.4, PEV.23, PEV.24, PEV.25 Ligand excluded by PLIP PEV.28: 13 residues within 4Å: Chain D: M.208, L.217, A.245, A.249, N.252, T.253, R.276 Chain G: R.65, N.116, V.117, F.120 Ligands: PEV.14, PEV.32 Ligand excluded by PLIP PEV.30: 10 residues within 4Å: Chain A: P.210, I.213, P.214 Chain G: A.205, R.208, V.209, Y.212, L.213 Ligands: PEV.2, NAD.27 Ligand excluded by PLIP PEV.31: 7 residues within 4Å: Chain C: F.238 Chain D: F.238 Chain G: V.110, P.113, N.116 Ligands: PEV.12, PEV.32 Ligand excluded by PLIP PEV.32: 5 residues within 4Å: Chain G: P.113, L.114, V.117 Ligands: PEV.28, PEV.31 Ligand excluded by PLIP PEV.33: 11 residues within 4Å: Chain A: A.245, A.248, A.249, N.252, T.253, R.276 Chain H: R.65, N.116, V.117, F.120 Ligands: PEV.37 Ligand excluded by PLIP PEV.34: 10 residues within 4Å: Chain B: T.221, D.225, W.240, Y.241, R.244, A.245 Chain H: R.105, R.107 Ligands: PEV.4, PEV.5 Ligand excluded by PLIP PEV.36: 9 residues within 4Å: Chain D: P.210, P.214 Chain H: A.205, R.208, V.209, Y.212, L.213 Ligands: PEV.13, NAD.21 Ligand excluded by PLIP PEV.37: 6 residues within 4Å: Chain H: P.113, L.114, V.117 Ligands: PEV.1, PEV.3, PEV.33 Ligand excluded by PLIP PEV.38: 5 residues within 4Å: Chain A: F.238 Chain H: V.110, P.113 Ligands: PEV.1, PEV.25 Ligand excluded by PLIP

4 x 8PP: 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL(Non-covalent)

8PP.6: 20 residues within 4Å: Chain B: M.208, P.210 Chain E: V.198 Chain F: A.58, G.59, G.62, W.115, L.118, G.119, A.121, L.122, G.125, T.126, L.199, I.202, I.203, G.206, C.207, A.210, I.211 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:W.115, F:W.115, F:T.126, F:L.199, F:I.202, F:A.210, F:I.211, B:P.210 pi-Stacking: F:W.115 8PP.18: 18 residues within 4Å: Chain C: M.208, P.210 Chain E: A.58, G.59, G.62, I.66, W.115, L.118, L.122, G.125, T.126, L.199, I.202, I.203, G.206, C.207, A.210, I.211 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.66, E:W.115, E:W.115, E:L.122, E:L.122, E:L.199, E:I.202, E:I.203, E:A.210, E:I.211 pi-Stacking: E:W.115 8PP.29: 19 residues within 4Å: Chain D: M.208, I.213 Chain G: A.58, G.59, G.62, I.66, W.115, L.118, G.119, A.121, L.122, G.125, T.126, I.202, I.203, G.206, C.207, A.210, I.211 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:W.115, G:W.115, G:L.122, G:I.202, G:I.203, G:A.210, G:I.211, D:I.213 pi-Stacking: G:W.115 8PP.35: 19 residues within 4Å: Chain A: M.208, I.213 Chain H: A.58, G.59, G.62, I.66, W.115, L.118, G.119, A.121, L.122, G.125, L.129, L.199, I.203, G.206, C.207, A.210, I.211 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:W.115, H:W.115, H:L.118, H:A.121, H:L.122, H:L.122, H:L.129, H:I.203, H:A.210, H:I.211, A:I.213 pi-Stacking: H:W.115

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.21: 10 residues within 4Å: Chain E: R.51, Y.212, R.216 Chain H: R.51, Y.212, R.216 Ligands: PEV.5, PEV.13, PEV.19, PEV.36 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain H Hydrogen bonds: E:R.51, E:R.51, E:R.216, H:R.51, H:R.51, H:R.216 Salt bridges: E:R.216, E:R.216, H:R.216, H:R.216 Hydrophobic interactions: H:Y.212 NAD.27: 11 residues within 4Å: Chain F: R.51, Y.212, E.215, R.216 Chain G: R.51, Y.212, E.215, R.216 Ligands: PEV.2, PEV.11, PEV.30 13 PLIP interactions: 8 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:R.51, F:Y.212, F:R.216, G:R.51, G:Y.212, G:R.216 Salt bridges: F:R.51, F:R.216, F:R.216, G:R.216 pi-Stacking: F:Y.212, F:Y.212 Hydrophobic interactions: G:Y.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manicki, M. et al., Structure and functionality of a multimeric human COQ7:COQ9 complex. Mol.Cell (2022)

Release Date

2022-11-02

Peptides

Ubiquinone biosynthesis protein COQ9, mitochondrial: ABCD
5-demethoxyubiquinone hydroxylase, mitochondrial: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Ubiquinone biosynthesis protein COQ9, mitochondrial

5-demethoxyubiquinone hydroxylase, mitochondrial

Related Entries With Identical Sequence