SMTL ID : 8eff.1

CryoEM of the soluble OPA1 tetramer from the GDP-AlFx bound helical assembly on a lipid membrane

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 24 residues within 4Å: Chain A: Q.103, G.106, T.108, S.109, E.112, R.122, G.123, S.124, M.128, T.129, T.273, K.274, D.276, L.277, K.280, V.308, T.309, G.310, G.312, N.313, S.314 Ligands: ALF.2, MG.3, K.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.106, A:T.108, A:T.108, A:K.274, A:G.310, A:G.312, A:G.312, A:N.313 Salt bridges: A:D.276 GDP.5: 24 residues within 4Å: Chain B: S.104, A.105, G.106, K.107, T.108, S.109, P.121, R.122, G.123, E.126, M.127, M.128, T.129, T.273, K.274, D.276, T.309, G.310, K.311, N.313, S.314 Ligands: ALF.6, MG.7, K.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.108, B:T.108, B:S.109, B:G.123, B:M.128, B:T.129, B:T.129, B:K.274, B:T.309, B:T.309 Salt bridges: B:D.276 pi-Cation interactions: B:K.274 GDP.9: 24 residues within 4Å: Chain C: Q.103, G.106, T.108, S.109, E.112, R.122, G.123, S.124, M.128, T.129, T.273, K.274, D.276, L.277, K.280, V.308, T.309, G.310, G.312, N.313, S.314 Ligands: ALF.10, MG.11, K.12 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.106, C:T.108, C:T.108, C:K.274, C:G.310, C:G.312, C:G.312, C:N.313 Salt bridges: C:D.276 GDP.13: 24 residues within 4Å: Chain D: S.104, A.105, G.106, K.107, T.108, S.109, P.121, R.122, G.123, E.126, M.127, M.128, T.129, T.273, K.274, D.276, T.309, G.310, K.311, N.313, S.314 Ligands: ALF.14, MG.15, K.16 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.108, D:T.108, D:S.109, D:G.123, D:M.128, D:T.129, D:T.129, D:K.274, D:T.309, D:T.309 Salt bridges: D:D.276 pi-Cation interactions: D:K.274

4 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 12 residues within 4Å: Chain A: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.1, MG.3, K.4 No protein-ligand interaction detected (PLIP) ALF.6: 14 residues within 4Å: Chain B: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.5, MG.7, K.8 No protein-ligand interaction detected (PLIP) ALF.10: 12 residues within 4Å: Chain C: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.9, MG.11, K.12 No protein-ligand interaction detected (PLIP) ALF.14: 14 residues within 4Å: Chain D: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.13, MG.15, K.16 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: T.108, F.120, M.128, T.129 Ligands: GDP.1, ALF.2 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: K.107, T.129 Ligands: GDP.5, ALF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.129 MG.11: 6 residues within 4Å: Chain C: T.108, F.120, M.128, T.129 Ligands: GDP.9, ALF.10 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain D: K.107, T.129 Ligands: GDP.13, ALF.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.129

4 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: Q.103, S.104 Ligands: GDP.1, ALF.2 No protein-ligand interaction detected (PLIP) K.8: 7 residues within 4Å: Chain B: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.5, ALF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.103 K.12: 4 residues within 4Å: Chain C: Q.103, S.104 Ligands: GDP.9, ALF.10 No protein-ligand interaction detected (PLIP) K.16: 7 residues within 4Å: Chain D: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.13, ALF.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:Q.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nyenhuis, S.B. et al., OPA1 helical structures give perspective to mitochondrial dysfunction. Nature (2023)

Release Date

2023-06-28

Peptides

Dynamin-like 120 kDa protein, form S1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dynamin-like 120 kDa protein, form S1

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