SMTL ID : 6bno.1

Structure of bare actin filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.16, Q.139, D.156 Ligands: ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.156, A:D.156 MG.3: 3 residues within 4Å: Chain B: Q.139, D.156 Ligands: ADP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.156, B:D.156 MG.5: 5 residues within 4Å: Chain C: S.16, Q.139, D.156, V.161 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain D: S.16, Q.139 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain E: S.16, Q.139, D.156 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.156, E:D.156 MG.11: 4 residues within 4Å: Chain F: S.16, Q.139, H.163 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.163 MG.13: 4 residues within 4Å: Chain G: S.16, Q.139, D.156 Ligands: ADP.14 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:S.16, G:D.156, G:D.156 MG.15: 4 residues within 4Å: Chain H: S.16, Q.139, D.156 Ligands: ADP.16 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.156, H:D.156

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

ADP.2: 18 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:Q.139, A:R.212, A:K.215, A:G.304 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.4: 18 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:Q.139, B:Q.139, B:R.212, B:K.215, B:G.304 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.6: 17 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, Q.139, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.13, C:S.16, C:G.17, C:L.18, C:Q.139, C:D.159, C:R.212, C:K.215, C:G.304 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308 ADP.8: 17 residues within 4Å: Chain D: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.13, D:S.16, D:G.17, D:L.18, D:Q.139, D:D.159, D:K.215, D:G.304 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.10: 19 residues within 4Å: Chain E: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:D.13, E:S.16, E:G.17, E:L.18, E:L.18, E:Q.139, E:R.212, E:K.215, E:G.304, E:M.307 Salt bridges: E:K.20, E:K.20 pi-Stacking: E:Y.308 ADP.12: 17 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, Q.139, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:D.13, F:S.16, F:G.17, F:L.18, F:Q.139, F:R.212, F:K.215, F:E.216, F:G.304 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308 ADP.14: 18 residues within 4Å: Chain G: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.13 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.16, G:G.17, G:L.18, G:Q.139, G:Q.139, G:R.212, G:K.215, G:G.304, G:T.305, G:M.307 Salt bridges: G:K.20, G:K.20 pi-Stacking: G:Y.308 ADP.16: 19 residues within 4Å: Chain H: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:D.13, H:S.16, H:G.17, H:L.18, H:L.18, H:Q.139, H:R.212, H:K.215, H:G.304 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gurel, P.S. et al., Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity. Elife (2017)

Release Date

2018-01-10

Peptides

Actin, alpha skeletal muscle: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Actin, alpha skeletal muscle

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