SMTL ID : 8efr.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

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

GDP.1: 25 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 Chain J: V.282 Ligands: ALF.2, MG.3, K.36 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.4: 28 residues within 4Å: Chain B: S.104, A.105, G.106, K.107, T.108, S.109, P.121, R.122, G.123, S.124, E.126, M.127, M.128, T.129, T.273, K.274, D.276, V.307, T.309, G.310, K.311, N.313, S.314 Chain G: K.280, N.281, V.282 Ligands: ALF.5, MG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.108, B:T.108, B:S.109, B:R.122, B:G.123, B:M.128, B:T.129, B:K.274, B:T.309, B:T.309 Salt bridges: B:D.276 GDP.8: 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.9, MG.10, K.11 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.12: 29 residues within 4Å: Chain D: Q.103, S.104, A.105, G.106, K.107, T.108, S.109, P.121, R.122, G.123, S.124, G.125, E.126, M.128, T.273, K.274, D.276, V.307, T.309, G.310, K.311, G.312, N.313, S.314 Chain E: K.280, N.281, V.282 Ligands: ALF.13, MG.14 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain D Hydrogen bonds: E:N.281, D:K.107, D:T.108, D:T.108, D:G.123, D:G.125, D:E.126, D:M.128, D:K.274, D:T.309, D:K.311 Salt bridges: D:D.276 GDP.17: 24 residues within 4Å: Chain D: V.282 Chain E: G.106, T.108, S.109, E.112, R.122, G.123, S.124, M.128, T.273, K.274, D.276, L.277, K.280, V.308, T.309, G.310, K.311, G.312, N.313, S.314 Ligands: K.15, ALF.18, MG.19 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:T.108, E:T.108, E:G.123, E:G.123, E:K.274, E:G.310, E:G.312, E:G.312, E:N.313 Salt bridges: E:D.276 pi-Cation interactions: E:K.274 GDP.20: 24 residues within 4Å: Chain F: 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.21, MG.22, K.23 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:T.108, F:T.108, F:S.109, F:G.123, F:M.128, F:T.129, F:T.129, F:K.274, F:T.309, F:T.309 Salt bridges: F:D.276 pi-Cation interactions: F:K.274 GDP.24: 24 residues within 4Å: Chain B: V.282 Chain G: G.106, T.108, S.109, E.112, R.122, G.123, S.124, M.128, T.273, K.274, D.276, L.277, K.280, V.308, T.309, G.310, K.311, G.312, N.313, S.314 Ligands: ALF.25, MG.26, K.27 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:T.108, G:T.108, G:G.123, G:K.274, G:K.274, G:K.280, G:G.310, G:G.312, G:G.312, G:N.313 Salt bridges: G:D.276 pi-Cation interactions: G:K.274 GDP.28: 24 residues within 4Å: Chain H: 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.29, MG.30, K.31 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:T.108, H:T.108, H:S.109, H:G.123, H:M.128, H:T.129, H:T.129, H:K.274, H:T.309, H:T.309 Salt bridges: H:D.276 pi-Cation interactions: H:K.274 GDP.32: 24 residues within 4Å: Chain I: 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.33, MG.34, K.35 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:G.106, I:T.108, I:T.108, I:K.274, I:G.310, I:G.312, I:G.312, I:N.313 Salt bridges: I:D.276 GDP.37: 27 residues within 4Å: Chain A: K.280, N.281, V.282 Chain J: 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.38, MG.39, K.40 12 PLIP interactions: 11 interactions with chain J, 1 interactions with chain A Hydrogen bonds: J:T.108, J:T.108, J:S.109, J:G.123, J:M.128, J:T.129, J:T.129, J:K.274, J:T.309, J:T.309, A:K.280 Salt bridges: J:D.276 GDP.41: 24 residues within 4Å: Chain K: 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.42, MG.43, K.44 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:G.106, K:T.108, K:T.108, K:K.274, K:G.310, K:G.312, K:G.312, K:N.313 Salt bridges: K:D.276 GDP.45: 24 residues within 4Å: Chain L: 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.46, MG.47, K.48 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:T.108, L:T.108, L:S.109, L:G.123, L:M.128, L:T.129, L:T.129, L:K.274, L:T.309, L:T.309 Salt bridges: L:D.276 pi-Cation interactions: L:K.274 GDP.49: 24 residues within 4Å: Chain M: 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.50, MG.51, K.52 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:G.106, M:T.108, M:T.108, M:K.274, M:G.310, M:G.312, M:G.312, M:N.313 Salt bridges: M:D.276 GDP.53: 24 residues within 4Å: Chain N: 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.54, MG.55, K.56 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:T.108, N:T.108, N:S.109, N:G.123, N:M.128, N:T.129, N:T.129, N:K.274, N:T.309, N:T.309 Salt bridges: N:D.276 pi-Cation interactions: N:K.274 GDP.57: 24 residues within 4Å: Chain O: 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.58, MG.59, K.60 9 PLIP interactions: 9 interactions with chain O Hydrogen bonds: O:G.106, O:T.108, O:T.108, O:K.274, O:G.310, O:G.312, O:G.312, O:N.313 Salt bridges: O:D.276 GDP.61: 24 residues within 4Å: Chain P: 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.62, MG.63, K.64 12 PLIP interactions: 12 interactions with chain P Hydrogen bonds: P:T.108, P:T.108, P:S.109, P:G.123, P:M.128, P:T.129, P:T.129, P:K.274, P:T.309, P:T.309 Salt bridges: P:D.276 pi-Cation interactions: P:K.274 GDP.65: 24 residues within 4Å: Chain Q: 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.66, MG.67, K.68 9 PLIP interactions: 9 interactions with chain Q Hydrogen bonds: Q:G.106, Q:T.108, Q:T.108, Q:K.274, Q:G.310, Q:G.312, Q:G.312, Q:N.313 Salt bridges: Q:D.276 GDP.69: 24 residues within 4Å: Chain R: 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.70, MG.71, K.72 12 PLIP interactions: 12 interactions with chain R Hydrogen bonds: R:T.108, R:T.108, R:S.109, R:G.123, R:M.128, R:T.129, R:T.129, R:K.274, R:T.309, R:T.309 Salt bridges: R:D.276 pi-Cation interactions: R:K.274

18 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.36 No protein-ligand interaction detected (PLIP) ALF.5: 11 residues within 4Å: Chain B: D.102, Q.103, S.104, K.107, E.126, M.127, G.207 Chain G: D.248 Ligands: GDP.4, MG.6, K.7 No protein-ligand interaction detected (PLIP) ALF.9: 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.8, MG.10, K.11 No protein-ligand interaction detected (PLIP) ALF.13: 13 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.12, MG.14 No protein-ligand interaction detected (PLIP) ALF.18: 12 residues within 4Å: Chain E: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: K.15, GDP.17, MG.19 No protein-ligand interaction detected (PLIP) ALF.21: 14 residues within 4Å: Chain F: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.20, MG.22, K.23 No protein-ligand interaction detected (PLIP) ALF.25: 11 residues within 4Å: Chain G: D.102, Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.24 No protein-ligand interaction detected (PLIP) ALF.29: 14 residues within 4Å: Chain H: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.28, MG.30, K.31 No protein-ligand interaction detected (PLIP) ALF.33: 12 residues within 4Å: Chain I: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.32, MG.34, K.35 No protein-ligand interaction detected (PLIP) ALF.38: 13 residues within 4Å: Chain J: D.102, Q.103, S.104, K.107, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.37, MG.39, K.40 No protein-ligand interaction detected (PLIP) ALF.42: 12 residues within 4Å: Chain K: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.41, MG.43, K.44 No protein-ligand interaction detected (PLIP) ALF.46: 14 residues within 4Å: Chain L: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.45, MG.47, K.48 No protein-ligand interaction detected (PLIP) ALF.50: 12 residues within 4Å: Chain M: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.49, MG.51, K.52 No protein-ligand interaction detected (PLIP) ALF.54: 14 residues within 4Å: Chain N: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.53, MG.55, K.56 No protein-ligand interaction detected (PLIP) ALF.58: 12 residues within 4Å: Chain O: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.57, MG.59, K.60 No protein-ligand interaction detected (PLIP) ALF.62: 14 residues within 4Å: Chain P: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.61, MG.63, K.64 No protein-ligand interaction detected (PLIP) ALF.66: 12 residues within 4Å: Chain Q: Q.103, G.106, K.107, T.108, M.127, M.128, T.129, P.206, G.207 Ligands: GDP.65, MG.67, K.68 No protein-ligand interaction detected (PLIP) ALF.70: 14 residues within 4Å: Chain R: D.102, Q.103, S.104, K.107, E.126, M.127, M.128, T.129, L.205, P.206, G.207 Ligands: GDP.69, MG.71, K.72 No protein-ligand interaction detected (PLIP)

18 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.6: 7 residues within 4Å: Chain B: K.107, M.127, T.129, P.206, G.207 Ligands: GDP.4, ALF.5 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain C: T.108, F.120, M.128, T.129 Ligands: GDP.8, ALF.9 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain D: K.107, T.108, M.128, T.129 Ligands: GDP.12, ALF.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.129 MG.19: 6 residues within 4Å: Chain E: T.108, F.120, M.128, T.129 Ligands: GDP.17, ALF.18 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain F: K.107, T.129 Ligands: GDP.20, ALF.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.129 MG.26: 5 residues within 4Å: Chain G: T.108, F.120, M.128, T.129 Ligands: GDP.24 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.108 MG.30: 4 residues within 4Å: Chain H: K.107, T.129 Ligands: GDP.28, ALF.29 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.129 MG.34: 6 residues within 4Å: Chain I: T.108, F.120, M.128, T.129 Ligands: GDP.32, ALF.33 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain J: K.107, T.129 Ligands: GDP.37, ALF.38 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.129 MG.43: 6 residues within 4Å: Chain K: T.108, F.120, M.128, T.129 Ligands: GDP.41, ALF.42 No protein-ligand interaction detected (PLIP) MG.47: 4 residues within 4Å: Chain L: K.107, T.129 Ligands: GDP.45, ALF.46 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.129 MG.51: 6 residues within 4Å: Chain M: T.108, F.120, M.128, T.129 Ligands: GDP.49, ALF.50 No protein-ligand interaction detected (PLIP) MG.55: 4 residues within 4Å: Chain N: K.107, T.129 Ligands: GDP.53, ALF.54 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.129 MG.59: 6 residues within 4Å: Chain O: T.108, F.120, M.128, T.129 Ligands: GDP.57, ALF.58 No protein-ligand interaction detected (PLIP) MG.63: 4 residues within 4Å: Chain P: K.107, T.129 Ligands: GDP.61, ALF.62 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.129 MG.67: 6 residues within 4Å: Chain Q: T.108, F.120, M.128, T.129 Ligands: GDP.65, ALF.66 No protein-ligand interaction detected (PLIP) MG.71: 4 residues within 4Å: Chain R: K.107, T.129 Ligands: GDP.69, ALF.70 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.129

18 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.7: 6 residues within 4Å: Chain B: Q.103, A.105, G.125, K.274 Chain G: R.287 Ligands: ALF.5 Ligand excluded by PLIP K.11: 4 residues within 4Å: Chain C: Q.103, S.104 Ligands: GDP.8, ALF.9 Ligand excluded by PLIP K.15: 5 residues within 4Å: Chain D: D.248 Chain E: Q.103, S.104 Ligands: GDP.17, ALF.18 Ligand excluded by PLIP K.16: 2 residues within 4Å: Chain D: G.125 Chain E: A.278 Ligand excluded by PLIP K.23: 7 residues within 4Å: Chain F: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.20, ALF.21 Ligand excluded by PLIP K.27: 6 residues within 4Å: Chain B: D.248, S.284 Chain G: S.104, S.124, K.274 Ligands: GDP.24 Ligand excluded by PLIP K.31: 7 residues within 4Å: Chain H: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.28, ALF.29 Ligand excluded by PLIP K.35: 4 residues within 4Å: Chain I: Q.103, S.104 Ligands: GDP.32, ALF.33 Ligand excluded by PLIP K.36: 5 residues within 4Å: Chain A: Q.103, S.104 Chain J: D.248 Ligands: GDP.1, ALF.2 Ligand excluded by PLIP K.40: 7 residues within 4Å: Chain J: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.37, ALF.38 Ligand excluded by PLIP K.44: 4 residues within 4Å: Chain K: Q.103, S.104 Ligands: GDP.41, ALF.42 Ligand excluded by PLIP K.48: 7 residues within 4Å: Chain L: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.45, ALF.46 Ligand excluded by PLIP K.52: 4 residues within 4Å: Chain M: Q.103, S.104 Ligands: GDP.49, ALF.50 Ligand excluded by PLIP K.56: 7 residues within 4Å: Chain N: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.53, ALF.54 Ligand excluded by PLIP K.60: 4 residues within 4Å: Chain O: Q.103, S.104 Ligands: GDP.57, ALF.58 Ligand excluded by PLIP K.64: 7 residues within 4Å: Chain P: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.61, ALF.62 Ligand excluded by PLIP K.68: 4 residues within 4Å: Chain Q: Q.103, S.104 Ligands: GDP.65, ALF.66 Ligand excluded by PLIP K.72: 7 residues within 4Å: Chain R: Q.103, S.104, A.105, E.126, M.127 Ligands: GDP.69, ALF.70 Ligand excluded by PLIP

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: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
K

E
D

F
L

G
E

H
M

I
F

J
N

K
G

L
O

M
H

N
P

O
I

P
Q

Q
J

R
R

Dynamin-like 120 kDa protein, form S1

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