SMTL ID : 7pme.1

Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (AppNHp, central 3er/2er)

Coordinates

PDB Format

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: 15 residues within 4Å: Chain C: E.74, H.75, I.77, T.79, L.112, P.114, R.179 Chain F: I.289 Chain G: T.196, R.198, G.199, Y.200, S.201, E.207, Q.248 16 PLIP interactions: 10 interactions with chain G, 5 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:T.196, G:Y.200, G:Y.200, G:E.207, C:I.77, C:T.79, C:P.114 Hydrogen bonds: G:G.199, G:G.199, G:G.199, G:S.201, G:S.201, G:Q.248, C:E.74, C:E.74, F:R.292 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 14 residues within 4Å: Chain C: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, Q.248 Chain F: E.74, I.77, T.79, L.112, P.114, R.179 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain F Hydrophobic interactions: C:T.196, C:Y.200, C:Y.200, C:E.207, F:E.74, F:I.77, F:T.79, F:P.114 Hydrogen bonds: C:R.198, C:G.199, C:S.201, C:Q.248, F:E.74, F:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 7 residues within 4Å: Chain G: E.74, H.75, I.77, T.79, L.112, P.114, R.179 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:E.74, G:I.77, G:T.79, G:P.114 Hydrogen bonds: G:E.74

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 16 residues within 4Å: Chain A: I.99, Y.100, N.111, P.112, E.114, Y.119, S.165, G.166, A.167, G.168, K.169, T.170, V.171, N.216 Ligands: MG.5, MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.111, A:Y.119, A:S.165, A:G.166, A:A.167, A:G.168, A:K.169, A:K.169, A:T.170, A:T.170, A:T.170, A:V.171 ANP.9: 17 residues within 4Å: Chain D: I.99, Y.100, N.111, P.112, E.114, Y.119, S.165, G.166, A.167, G.168, K.169, T.170, V.171, N.216, S.218 Ligands: MG.10, MG.11 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.111, D:Y.119, D:S.165, D:G.166, D:A.167, D:G.168, D:T.170, D:T.170, D:V.171, D:S.218

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

MG.5: 3 residues within 4Å: Chain A: T.170, S.218 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: D.13, Q.139 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: T.170, S.218, D.437 Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain G: D.13, Q.139 Ligands: ADP.14 No protein-ligand interaction detected (PLIP)

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

ADP.7: 17 residues within 4Å: Chain C: G.15, S.16, 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.8 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.16, 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.12: 17 residues within 4Å: Chain F: G.15, S.16, 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 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.16, 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.14: 17 residues within 4Å: Chain G: G.15, S.16, 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.15 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:S.16, 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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

G
G

Unconventional myosin-Va

Myosin light chain 6B

Actin, alpha skeletal muscle

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