SMTL ID : 8sxz.1

Cryo-EM of the GDP-bound human dynamin 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: 22 residues within 4Å: Chain A: S.45, A.46, G.47, A.48, S.49, S.50, R.63, G.64, S.65, T.69, T.209, K.210, D.212, L.213, V.239, N.240, R.241, S.242, Q.243, I.246 Chain B: D.215 Ligands: MG.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.45, A:A.46, A:G.47, A:A.48, A:S.49, A:S.50, A:S.50, A:G.64, A:T.69, A:K.210, A:N.240, A:N.240, A:R.241 Salt bridges: A:D.212, B:D.215 GDP.3: 25 residues within 4Å: Chain A: D.215 Chain B: G.43, S.45, A.46, G.47, A.48, S.49, S.50, R.63, G.64, S.65, T.69, T.209, K.210, L.211, D.212, L.213, V.238, V.239, N.240, R.241, S.242, Q.243, I.246 Ligands: MG.4 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.44, B:S.45, B:A.46, B:G.47, B:A.48, B:S.49, B:S.49, B:S.50, B:G.64, B:K.210, B:N.240, B:N.240, B:R.241 Salt bridges: B:D.212, A:D.215 GDP.5: 23 residues within 4Å: Chain C: Q.44, S.45, A.46, G.47, A.48, S.49, S.50, R.63, G.64, S.65, T.69, T.209, K.210, D.212, L.213, V.239, N.240, R.241, S.242, Q.243, I.246 Chain D: D.215 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.45, C:G.47, C:A.48, C:S.49, C:S.49, C:S.50, C:S.50, C:G.64, C:T.69, C:K.210, C:N.240, C:N.240, C:R.241 Salt bridges: C:D.212, D:D.215 GDP.7: 24 residues within 4Å: Chain C: D.215 Chain D: G.43, S.45, A.46, G.47, A.48, S.49, S.50, R.63, G.64, S.65, T.69, T.209, K.210, L.211, D.212, L.213, V.239, N.240, R.241, S.242, Q.243, I.246 Ligands: MG.8 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.45, D:A.46, D:G.47, D:A.48, D:S.49, D:S.49, D:S.50, D:S.50, D:G.64, D:K.210, D:N.240, D:R.241 Salt bridges: D:D.212, C:D.215 pi-Cation interactions: D:K.210

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.49, T.69 Ligands: GDP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.49, A:T.69 MG.4: 3 residues within 4Å: Chain B: S.49, T.69 Ligands: GDP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.49, B:T.69 MG.6: 3 residues within 4Å: Chain C: S.49, T.69 Ligands: GDP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.49, C:T.69 MG.8: 3 residues within 4Å: Chain D: S.49, T.69 Ligands: GDP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.49, D:T.69

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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