SMTL ID : 8oid.1

Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the N111S mutation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.13, S.14, G.15, M.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, K.336 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:M.16, A:D.157, A:D.157, A:G.158, A:K.213, A:E.214, A:G.302, A:T.303, A:M.305, A:K.336 Water bridges: A:D.11, A:D.11, A:K.18, A:K.18, A:K.18, A:K.18, A:G.182, A:T.186 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306 ADP.3: 18 residues within 4Å: Chain B: G.13, S.14, G.15, M.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, K.336 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:M.16, B:D.157, B:D.157, B:G.158, B:K.213, B:E.214, B:G.302, B:T.303, B:M.305, B:K.336 Water bridges: B:D.11, B:N.12, B:K.18, B:K.18, B:K.18, B:K.18, B:T.186, B:K.213 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306 ADP.5: 18 residues within 4Å: Chain C: G.13, S.14, G.15, M.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, K.336 Ligands: MG.6 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:S.14, C:G.15, C:M.16, C:D.157, C:D.157, C:G.158, C:K.213, C:E.214, C:G.302, C:M.305, C:K.336 Water bridges: C:D.11, C:N.12, C:K.18, C:K.18, C:K.18, C:K.18, C:G.182, C:T.186 Salt bridges: C:K.18, C:K.18 pi-Stacking: C:Y.306 ADP.7: 18 residues within 4Å: Chain D: G.13, S.14, G.15, M.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, K.336 Ligands: MG.8 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:S.14, D:G.15, D:M.16, D:D.157, D:D.157, D:G.158, D:K.213, D:E.214, D:G.302, D:M.305, D:K.336 Water bridges: D:K.18, D:K.18, D:K.18, D:D.157, D:G.182 Salt bridges: D:K.18, D:K.18 pi-Stacking: D:Y.306 ADP.9: 18 residues within 4Å: Chain E: G.13, S.14, G.15, M.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, K.336 Ligands: MG.10 24 PLIP interactions: 24 interactions with chain E Hydrogen bonds: E:S.14, E:G.15, E:M.16, E:D.157, E:D.157, E:D.157, E:G.158, E:K.213, E:E.214, E:G.302, E:T.303, E:M.305, E:K.336 Water bridges: E:D.11, E:N.12, E:K.18, E:K.18, E:K.18, E:K.18, E:G.182, E:T.186 Salt bridges: E:K.18, E:K.18 pi-Stacking: E:Y.306

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

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