SMTL ID : 8t0k.1

Cryo-EM of the GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state

Coordinates

PDB Format Compare

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.50, S.51, A.52, G.53, A.54, S.55, S.56, R.69, G.70, S.71, V.74, T.75, T.215, K.216, D.218, L.219, V.245, N.246, R.247, S.248, Q.249, I.252 Chain B: D.221 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.51, A:G.53, A:G.53, A:A.54, A:S.55, A:S.55, A:S.56, A:G.70, A:G.70, A:K.216, A:N.246, A:N.246 Salt bridges: A:D.218, B:D.221 GDP.3: 23 residues within 4Å: Chain A: D.221 Chain B: Q.50, S.51, A.52, G.53, A.54, S.55, S.56, R.69, G.70, S.71, T.75, T.215, K.216, D.218, L.219, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.4 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.51, B:A.52, B:G.53, B:A.54, B:S.55, B:S.55, B:S.56, B:G.70, B:T.75, B:T.75, B:K.216, B:N.246, B:N.246, B:Q.249 Salt bridges: B:D.218, A:D.221 pi-Cation interactions: B:K.216 GDP.5: 23 residues within 4Å: Chain C: G.49, S.51, A.52, G.53, A.54, S.55, S.56, R.69, G.70, S.71, T.75, T.215, K.216, D.218, L.219, V.245, N.246, R.247, S.248, Q.249, I.252 Chain D: D.221 Ligands: MG.6 16 PLIP interactions: 1 interactions with chain D, 15 interactions with chain C Salt bridges: D:D.221 Hydrogen bonds: C:G.49, C:S.51, C:G.53, C:A.54, C:S.55, C:S.55, C:S.56, C:S.56, C:G.70, C:T.75, C:K.216, C:D.218, C:N.246, C:N.246, C:Q.249 GDP.7: 24 residues within 4Å: Chain C: D.221 Chain D: Q.50, S.51, A.52, G.53, A.54, S.55, S.56, R.69, G.70, S.71, T.75, T.215, K.216, L.217, D.218, L.219, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.8 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.51, D:A.52, D:G.53, D:A.54, D:S.55, D:S.55, D:S.56, D:S.56, D:G.70, D:T.75, D:T.75, D:K.216, D:N.246, D:N.246, D:R.247 Salt bridges: D:D.218, C:D.221 pi-Cation interactions: D:K.216

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: S.55, T.75 Ligands: GDP.1 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain B: S.55, P.68, R.69, V.74, T.75, D.146 Ligands: GDP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.55, B:T.75 MG.6: 3 residues within 4Å: Chain C: S.55, T.75 Ligands: GDP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.55, C:T.75 MG.8: 5 residues within 4Å: Chain D: Q.50, S.51, A.54, S.55 Ligands: GDP.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jimah, J.R. et al., Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission. Dev.Cell (2024)

Release Date

2024-05-01

Peptides

Dynamin-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
b

B
c

C
f

D
g

Dynamin-1

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