SMTL ID : 8oi6.1

Cryo-EM structure of the undecorated barbed end of filamentous beta/gamma actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

3 x TRP- EEP- ALA- DTH- CYS- HYP- ALA: PHALLOIDIN(Non-covalent)

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 14 residues within 4Å: Chain A: E.72, I.75, T.77, L.110, P.112, R.177 Chain B: R.196, G.197, Y.198, S.199, E.205, L.242, Q.246, I.248 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.198, B:L.242, B:I.248, A:E.72, A:I.75, A:T.77, A:P.112 Hydrogen bonds: B:G.197, B:G.197, B:G.197, B:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 17 residues within 4Å: Chain A: V.287, R.290 Chain B: E.72, I.75, T.77, L.110, P.112, R.177, D.179 Chain C: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246 13 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:L.242, A:V.287, B:I.75, B:I.75, B:T.77, B:P.112 Hydrogen bonds: C:G.197, C:G.197, C:G.197, C:S.199, C:Q.246, A:R.290, A:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 16 residues within 4Å: Chain B: V.287, R.290 Chain C: E.72, I.75, T.77, L.110, P.112, R.177 Chain D: T.194, R.196, G.197, Y.198, S.199, E.205, Q.246, I.248 16 PLIP interactions: 8 interactions with chain D, 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: D:Y.198, D:Y.198, D:I.248, B:V.287, C:E.72, C:I.75, C:T.77, C:P.112 Hydrogen bonds: D:G.197, D:G.197, D:G.197, D:S.199, D:Q.246, B:R.290, B:R.290, C:E.72

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

ADP.4: 16 residues within 4Å: Chain A: G.13, S.14, G.15, M.16, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.15, A:M.16, 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, A:K.336 ADP.6: 17 residues within 4Å: Chain B: G.13, S.14, G.15, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.15, B:M.16, B:D.157, B:D.157, B:K.213, B:E.214, B:G.302 Salt bridges: B:K.18, B:K.18, B:K.336 ADP.8: 17 residues within 4Å: Chain C: G.13, S.14, G.15, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.14, C:G.15, C:M.16, C:D.157, C:D.157, C:K.213, C:E.214, C:G.302 Salt bridges: C:K.18, C:K.18 ADP.10: 16 residues within 4Å: Chain D: G.13, S.14, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.11 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:M.16, D:D.157, D:D.157, D:D.157, D:R.210, D:K.213, D:E.214, D:G.302 Salt bridges: D:K.18, D:K.18

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: Q.137 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: K.18 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: K.18, Q.137 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain D: Q.137, D.154 Ligands: ADP.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-08-09

Peptides

Actin, cytoplasmic 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Actin, cytoplasmic 1

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