SMTL ID : 9fjm.1

Cryo-EM structure of the phalloidin-bound pointed end of the actin filament.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x TRP- EEP- ALA- DTH- CYS- HYP- ALA: Phalloidin

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 13 residues within 4Å: Chain A: E.71, I.74, L.109, P.111, R.176 Chain B: T.193, G.196, Y.197, S.198, E.204, L.241, Q.245, I.247 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.241, B:I.247, A:I.74, A:P.111 Hydrogen bonds: B:G.196, B:G.196, B:S.198 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 13 residues within 4Å: Chain A: R.289 Chain B: E.71, I.74, L.109, P.111, R.176 Chain C: G.196, Y.197, S.198, E.204, L.241, Q.245, I.247 13 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:Y.197, C:L.241, C:I.247, B:E.71, B:I.74, B:P.111 Hydrogen bonds: C:G.196, C:G.196, C:G.196, C:S.198, C:Q.245, A:R.289, A:R.289 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 6 residues within 4Å: Chain C: V.286, R.289 Chain D: E.71, I.74, P.111, R.176 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.286, D:I.74, D:P.111 Hydrogen bonds: C:R.289, C:R.289 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 17 residues within 4Å: Chain B: V.286, R.289 Chain C: E.71, I.74, L.109, P.111, R.176, D.178 Chain D: T.193, R.195, G.196, Y.197, S.198, F.199, E.204, L.241, Q.245 13 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: D:Y.197, D:Y.197, D:L.241, B:V.286, C:I.74, C:I.74, C:P.111 Hydrogen bonds: D:G.196, D:G.196, D:G.196, D:S.198, D:Q.245, B:R.289

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

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

4 x MG: MAGNESIUM ION

MG.6: 4 residues within 4Å: Chain A: D.153, V.338 Ligands: ADP.5, PO4.7 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: Q.136, D.153 Ligands: ADP.8, PO4.10 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: Q.136, D.153 Ligands: ADP.11, PO4.13 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain D: D.10, K.17 Ligands: ADP.14, PO4.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.10

4 x PO4: PHOSPHATE ION

PO4.7: 7 residues within 4Å: Chain A: Q.136, D.153, G.155, D.156, H.160 Ligands: ADP.5, MG.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.136, A:Q.136, A:D.153, A:G.155, A:D.156 Salt bridges: A:H.160 PO4.10: 8 residues within 4Å: Chain B: G.12, S.13, Q.136, D.156, G.157, V.158 Ligands: ADP.8, MG.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.13, B:Q.136, B:Q.136, B:D.156, B:G.157 PO4.13: 9 residues within 4Å: Chain C: G.12, S.13, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.11, MG.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.13, C:S.13, C:S.13, C:Q.136, C:D.156, C:G.157, C:V.158 PO4.16: 10 residues within 4Å: Chain D: S.13, Q.136, D.153, G.155, D.156, G.157, V.158, H.160 Ligands: ADP.14, MG.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.13, D:Q.136, D:G.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boiero Sanders, M. et al., Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly. Nat Commun (2024)

Release Date

2024-09-11

Peptides

Actin, cytoplasmic 1, N-terminally processed: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Actin, cytoplasmic 1, N-terminally processed

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