SMTL ID : 7plu.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-2-mer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 12 residues within 4Å: Chain B: E.74, I.77, P.114, R.179 Chain E: I.289 Chain G: T.196, R.198, G.199, Y.200, S.201, E.207, Q.248 11 PLIP interactions: 6 interactions with chain G, 3 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: G:T.196, G:Y.200, B:E.74, B:I.77, B:P.114, E:I.289 Hydrogen bonds: G:G.199, G:S.201, G:S.201, G:Q.248, E:R.292 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 13 residues within 4Å: Chain B: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain E: E.74, I.77, P.114, R.179 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain B Hydrophobic interactions: E:E.74, E:I.77, E:P.114, B:T.196, B:Y.200, B:F.202, B:L.244 Hydrogen bonds: B:G.199, B:S.201, B:S.201, B:Q.248 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 6 residues within 4Å: Chain B: I.289 Chain G: E.74, I.77, T.79, P.114, R.179 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:E.74, G:I.77, G:T.79, G:P.114

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

ADP.4: 17 residues within 4Å: Chain B: 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.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.16, B:L.18, B:D.159, B:D.159, B:R.212, B:K.215, B:E.216, B:G.304, B:T.305 Salt bridges: B:K.20, B:K.20 ADP.6: 17 residues within 4Å: Chain E: 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.7 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.16, E:L.18, E:D.159, E:D.159, E:R.212, E:K.215, E:E.216, E:G.304, E:T.305 Salt bridges: E:K.20, E:K.20 ADP.8: 17 residues within 4Å: Chain G: G.15, S.16, L.18, K.20, G.158, D.159, G.184, R.185, R.212, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:S.16, 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, G:K.338

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain B: Q.139 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: Q.139 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain G: G.158 Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

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
Actin, alpha skeletal muscle: BEG
Myosin light chain 6B: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
C

E
F

G
G

C
B

F
E

Unconventional myosin-Va

Actin, alpha skeletal muscle

Myosin light chain 6B

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