SMTL ID : 9qew.1

Cryo-EM structure of the undecorated actin filament in the ADP-Pi state.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 19 residues within 4Å: Chain A: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.2, PO4.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.13, A:G.14, A:M.15, A:D.156, A:D.156, A:K.212, A:G.301, A:M.304 Water bridges: A:G.12, A:G.12, A:D.156, A:G.181, A:Y.305 Salt bridges: A:K.17 pi-Stacking: A:Y.305 ADP.4: 19 residues within 4Å: Chain B: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.5, PO4.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.13, B:G.14, B:M.15, B:D.156, B:D.156, B:K.212, B:G.301, B:M.304 Water bridges: B:D.10, B:G.12, B:G.12, B:D.156, B:G.181, B:Y.305 Salt bridges: B:K.17 pi-Stacking: B:Y.305 ADP.7: 19 residues within 4Å: Chain C: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.8, PO4.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.13, C:G.14, C:M.15, C:D.156, C:D.156, C:K.212, C:G.301, C:M.304 Water bridges: C:D.10, C:G.12, C:G.12, C:Y.305 Salt bridges: C:K.17 pi-Stacking: C:Y.305 ADP.10: 19 residues within 4Å: Chain D: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.11, PO4.12 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.13, D:G.14, D:M.15, D:D.156, D:D.156, D:K.212, D:G.301, D:M.304 Water bridges: D:D.10, D:G.12, D:G.12, D:Y.305 Salt bridges: D:K.17 pi-Stacking: D:Y.305 ADP.13: 19 residues within 4Å: Chain E: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.14, PO4.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.13, E:G.14, E:M.15, E:D.156, E:D.156, E:K.212, E:G.301, E:M.304 Water bridges: E:G.12, E:G.12, E:Y.305 Salt bridges: E:K.17 pi-Stacking: E:Y.305

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 2 residues within 4Å: Ligands: ADP.1, PO4.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Ligands: ADP.4, PO4.6 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Ligands: ADP.7, PO4.9 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Ligands: ADP.10, PO4.12 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Ligands: ADP.13, PO4.15 No protein-ligand interaction detected (PLIP)

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 10 residues within 4Å: Chain A: G.12, S.13, G.73, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.13, A:Q.136, A:G.155, A:D.156, A:G.157, A:V.158, A:V.158 Water bridges: A:D.153 PO4.6: 10 residues within 4Å: Chain B: G.12, S.13, G.73, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.4, MG.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.13, B:Q.136, B:G.155, B:D.156, B:G.157, B:V.158, B:V.158 Water bridges: B:D.153 PO4.9: 10 residues within 4Å: Chain C: G.12, S.13, G.73, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.7, MG.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.13, C:Q.136, C:G.155, C:D.156, C:G.157, C:V.158, C:V.158 Water bridges: C:D.153 PO4.12: 10 residues within 4Å: Chain D: G.12, S.13, G.73, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.10, MG.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.13, D:Q.136, D:G.155, D:D.156, D:G.157, D:V.158, D:V.158 Water bridges: D:D.153 PO4.15: 10 residues within 4Å: Chain E: G.12, S.13, G.73, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.13, MG.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.13, E:Q.136, E:G.155, E:D.156, E:G.157, E:V.158, E:V.158 Water bridges: E:D.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Choreography of rapid actin filament disassembly by coronin, cofilin and AIP1. To Be Published

Release Date

2025-10-08

Peptides

Actin, cytoplasmic 1, N-terminally processed: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

E
E

Actin, cytoplasmic 1, N-terminally processed

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