SMTL ID : 7r8v.1

Cryo-EM structure of the ADP state actin filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.10, A:G.11, A:L.12, A:D.153, A:D.153, A:K.209, A:E.210, A:G.298, A:T.299, A:M.301 Salt bridges: A:K.14, A:K.14, A:K.332 pi-Stacking: A:Y.302 ADP.3: 17 residues within 4Å: Chain B: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.10, B:G.11, B:L.12, B:D.153, B:D.153, B:K.209, B:E.210, B:G.298, B:T.299, B:M.301 Salt bridges: B:K.14, B:K.14, B:K.332 pi-Stacking: B:Y.302 ADP.5: 17 residues within 4Å: Chain C: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.10, C:G.11, C:L.12, C:D.153, C:D.153, C:K.209, C:E.210, C:G.298, C:T.299, C:M.301 Salt bridges: C:K.14, C:K.14, C:K.332 pi-Stacking: C:Y.302 ADP.7: 17 residues within 4Å: Chain D: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.10, D:G.11, D:L.12, D:D.153, D:D.153, D:K.209, D:E.210, D:G.298, D:T.299, D:M.301 Salt bridges: D:K.14, D:K.14, D:K.332 pi-Stacking: D:Y.302 ADP.9: 17 residues within 4Å: Chain E: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.10, E:G.11, E:L.12, E:D.153, E:D.153, E:K.209, E:E.210, E:G.298, E:T.299, E:M.301 Salt bridges: E:K.14, E:K.14, E:K.332 pi-Stacking: E:Y.302

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.133 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.133 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: Q.133 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: Q.133 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: Q.133 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, R. et al., Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia. Sci Adv (2022)

Release Date

2021-07-28

Peptides

Actin, alpha skeletal muscle, intermediate form: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

Actin, alpha skeletal muscle, intermediate form

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