SMTL ID : 7pm6.1

Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 3er/2er)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-mer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 13 residues within 4Å: Chain C: E.74, H.75, I.77, T.79, P.114, R.179 Chain F: I.289 Chain G: R.198, G.199, Y.200, S.201, E.207, Q.248 12 PLIP interactions: 7 interactions with chain G, 4 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:Y.200, C:E.74, C:I.77, C:T.79, C:P.114, F:I.289 Hydrogen bonds: G:R.198, G:G.199, G:S.201, G:S.201, G:S.201, G:Q.248 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 12 residues within 4Å: Chain C: R.198, G.199, Y.200, S.201, F.202, Q.248 Chain F: E.74, H.75, I.77, T.79, P.114, R.179 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain F Hydrophobic interactions: C:Y.200, C:Y.200, C:F.202, F:E.74, F:I.77, F:T.79, F:P.114 Hydrogen bonds: C:G.199, C:G.199, C:S.201, C:S.201, C:S.201, C:S.201, C:Q.248 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 7 residues within 4Å: Chain C: R.292 Chain G: E.74, H.75, I.77, T.79, P.114, R.179 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:E.74, G:I.77, G:T.79, G:P.114 Hydrogen bonds: C:R.292, C:R.292

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

MG.4: 3 residues within 4Å: Chain B: T.170, S.218 Ligands: ADP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.170, B:S.218 MG.7: 3 residues within 4Å: Chain C: D.156, G.158 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain E: T.170, S.218 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.170, E:S.218 MG.11: 1 residues within 4Å: Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP)

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

ADP.5: 13 residues within 4Å: Chain B: N.111, P.112, Y.113, E.114, Y.119, S.165, G.166, A.167, G.168, K.169, T.170, V.171 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.111, B:Y.119, B:G.166, B:G.168, B:K.169, B:T.170, B:V.171 Salt bridges: B:K.169 ADP.6: 18 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:D.159, C:D.159, C:R.212, C:K.215, C:E.216, C:G.304, C:T.305 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308 ADP.9: 14 residues within 4Å: Chain E: Y.100, N.111, P.112, Y.113, E.114, Y.119, S.165, G.166, A.167, G.168, K.169, T.170, V.171 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:N.111, E:Y.119, E:G.166, E:G.168, E:K.169, E:T.170, E:T.170, E:V.171 Salt bridges: E:K.169 ADP.10: 18 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.16, F:G.17, F:L.18, F:D.159, F:D.159, F:R.212, F:K.215, F:E.216, F:G.304, F:T.305 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308 ADP.12: 18 residues within 4Å: Chain G: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.13 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.16, G:G.17, G:L.18, G:D.159, G:D.159, G:R.212, G:K.215, G:E.216, G:G.304, G:T.305 Salt bridges: G:K.20, G:K.20 pi-Stacking: G:Y.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pospich, S. et al., High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. Elife (2021)

Release Date

2021-12-22

Peptides

Myosin light chain 6B: AD
Unconventional myosin-Va: BE
Actin, alpha skeletal muscle: CFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
E

B
A

E
D

C
C

F
F

G
G

Myosin light chain 6B

Unconventional myosin-Va

Actin, alpha skeletal muscle

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