SMTL ID : 9duv.1

Cryo-EM structure of recombinant R254H ACTA1 phalloidin-stabilized F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 7 residues within 4Å: Chain A: E.72, I.75, L.110, P.112, R.177 Chain B: I.287, R.290 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.287, A:I.75, A:I.75, A:P.112 Hydrogen bonds: B:R.290, B:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 13 residues within 4Å: Chain A: T.194, R.196, G.197, Y.198, S.199, L.242, I.248 Chain B: E.72, I.75, L.110, P.112, R.177 Chain C: I.287 12 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:T.194, A:Y.198, A:L.242, A:I.248, B:I.75, B:P.112, C:I.287 Hydrogen bonds: A:G.197, A:G.197, A:G.197, A:S.199, C:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 14 residues within 4Å: Chain B: R.196, G.197, Y.198, F.200, E.205, L.242, Q.246, I.248 Chain C: E.72, I.75, L.110, P.112, R.177 Chain D: I.287 8 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: B:Y.198, B:Y.198, B:F.200, B:L.242, B:I.248, C:P.112, D:I.287 Hydrogen bonds: B:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 13 residues within 4Å: Chain C: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, I.248 Chain D: E.72, I.75, L.110, R.177 Chain E: I.287 10 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: C:T.194, C:Y.198, C:L.242, C:I.248, D:I.75, E:I.287 Hydrogen bonds: C:G.197, C:G.197, C:G.197, C:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.5: 14 residues within 4Å: Chain D: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, I.248 Chain E: E.72, I.75, L.110, R.177 Chain F: I.287, R.290 12 PLIP interactions: 8 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: D:T.194, D:Y.198, D:L.242, D:I.248, F:I.287, E:I.75, E:I.75 Hydrogen bonds: D:G.197, D:G.197, D:G.197, D:S.199, F:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.6: 12 residues within 4Å: Chain E: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, I.248 Chain F: E.72, T.77, L.110, P.112 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:T.194, E:Y.198, E:Y.198, E:L.242, E:I.248, F:P.112 Hydrogen bonds: E:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.7: 9 residues within 4Å: Chain F: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246, I.248 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:T.194, F:Y.198, F:Y.198, F:L.242, F:I.248 Hydrogen bonds: F:G.197, F:G.197, F:G.197, F:S.199, F:Q.246

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

ADP.8: 15 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, Y.306, K.336 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.14, A:L.16, A:L.16, A:D.157, A:D.157, A:D.157, A:K.213, A:E.214, A:G.302, A:T.303 Salt bridges: A:K.18, A:K.18 ADP.10: 18 residues within 4Å: Chain B: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, G.182, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.11 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.14, B:S.14, B:L.16, B:L.16, B:S.155, B:D.157, B:D.157, B:D.157, B:K.213, B:E.214, B:G.302, B:T.303 Salt bridges: B:K.18, B:K.18 ADP.12: 18 residues within 4Å: Chain C: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, Y.306, K.336 Ligands: MG.13 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.14, C:S.14, C:L.16, C:L.16, C:S.155, C:D.157, C:D.157, C:D.157, C:K.213, C:E.214, C:G.302, C:T.303, C:K.336 Salt bridges: C:K.18, C:K.18 ADP.14: 17 residues within 4Å: Chain D: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, G.182, K.213, E.214, G.301, G.302, T.303, Y.306, K.336 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.14, D:S.14, D:L.16, D:L.16, D:S.155, D:D.157, D:D.157, D:D.157, D:K.213, D:E.214, D:G.302, D:T.303 Salt bridges: D:K.18, D:K.18 ADP.16: 17 residues within 4Å: Chain E: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, G.182, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.17 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.14, E:L.16, E:S.155, E:D.157, E:D.157, E:D.157, E:K.213, E:G.302, E:T.303 Salt bridges: E:K.18 ADP.18: 16 residues within 4Å: Chain F: G.13, S.14, G.15, L.16, K.18, D.157, G.182, K.213, E.214, G.302, T.303, M.305, Y.306, P.307, K.336 Ligands: MG.19 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:L.16, F:D.157, F:D.157, F:D.157, F:K.213, F:K.213, F:G.302, F:T.303, F:K.336 Salt bridges: F:K.18, F:K.18, F:K.336

6 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: Q.137, D.154 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: Q.137 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: Q.137, D.154 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: Q.137, D.154 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain E: Q.137, D.154 Ligands: ADP.16 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain F: Q.137, D.154 Ligands: ADP.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garg, A. et al., Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-10-23

Peptides

Actin, alpha skeletal muscle: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Actin, alpha skeletal muscle