SMTL ID : 6t1y.1

Cryo-EM structure of phalloidin-stabilized F-actin (copolymerized)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x TRP- EEP- ALA- DTH- CYS- HYP- ALA: phalloidin(Non-covalent)

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 10 residues within 4Å: Chain A: E.72, H.73, I.75, T.77, L.110, P.112, R.177, D.179 Chain B: I.287, R.290 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.287, A:I.75, A:P.112 Hydrogen bonds: B:R.290, B:R.290, A:E.72, A:E.72 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 17 residues within 4Å: Chain A: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246 Chain B: E.72, I.75, T.77, L.110, P.112, R.177, D.179 Chain C: I.287, R.290 14 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:I.75, B:P.112, A:T.194, A:Y.198, A:L.242, C:I.287 Hydrogen bonds: B:E.72, B:E.72, A:G.197, A:G.197, A:G.197, A:S.199, C:R.290, C:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 17 residues within 4Å: Chain B: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246 Chain C: E.72, I.75, T.77, L.110, P.112, R.177, D.179 Chain D: I.287, R.290 14 PLIP interactions: 4 interactions with chain C, 7 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:I.75, C:P.112, B:T.194, B:Y.198, B:L.242, D:I.287 Hydrogen bonds: C:E.72, C:E.72, B:G.197, B:G.197, B:G.197, B:S.199, D:R.290, D:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 18 residues within 4Å: Chain C: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246 Chain D: E.72, H.73, I.75, T.77, L.110, P.112, R.177, D.179 Chain E: I.287, R.290 14 PLIP interactions: 3 interactions with chain E, 7 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: E:I.287, C:T.194, C:Y.198, C:L.242, D:I.75, D:P.112 Hydrogen bonds: E:R.290, E:R.290, C:G.197, C:G.197, C:G.197, C:S.199, D:E.72, D:E.72 TRP-EEP-ALA-DTH-CYS-HYP-ALA.5: 16 residues within 4Å: Chain D: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246 Chain E: E.72, H.73, I.75, T.77, L.110, P.112, R.177, D.179 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:T.194, D:Y.198, D:L.242, E:I.75, E:P.112 Hydrogen bonds: D:G.197, D:G.197, D:G.197, D:S.199, E:E.72, E:E.72

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

ADP.6: 16 residues within 4Å: Chain A: G.13, S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.16, A:D.157, A:D.157, A:D.157, A:K.213, A:E.214, A:E.214, A:G.302 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306 ADP.8: 16 residues within 4Å: Chain B: G.13, S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:L.16, B:D.157, B:D.157, B:D.157, B:K.213, B:E.214, B:E.214, B:G.302 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306 ADP.10: 16 residues within 4Å: Chain C: G.13, S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:L.16, C:D.157, C:D.157, C:D.157, C:K.213, C:E.214, C:E.214, C:G.302 Salt bridges: C:K.18, C:K.18 pi-Stacking: C:Y.306 ADP.12: 16 residues within 4Å: Chain D: G.13, S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.13 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:L.16, D:D.157, D:D.157, D:D.157, D:K.213, D:E.214, D:E.214, D:G.302 Salt bridges: D:K.18, D:K.18 pi-Stacking: D:Y.306 ADP.14: 16 residues within 4Å: Chain E: G.13, S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:L.16, E:D.157, E:D.157, E:D.157, E:K.213, E:E.214, E:E.214, E:G.302 Salt bridges: E:K.18, E:K.18 pi-Stacking: E:Y.306

5 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: Q.137, D.154 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: Q.137, D.154 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: Q.137, D.154 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: Q.137, D.154 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain E: Q.137, D.154 Ligands: ADP.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pospich, S. et al., Structural Effects and Functional Implications of Phalloidin and Jasplakinolide Binding to Actin Filaments. Structure (2020)

Release Date

2020-03-04

Peptides

Actin, alpha skeletal muscle: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Actin, alpha skeletal muscle

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