SMTL ID : 7plz.1

Cryo-EM structure of the actomyosin-V complex in the rigor state (central 3er/2er, young JASP-stabilized F-actin)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-2-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain B: 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: PO4.2, MG.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.159, B:D.159, B:R.212, B:K.215, B:E.216, B:G.304, B:T.305, B:K.338 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.6: 19 residues within 4Å: Chain E: 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: PO4.7, MG.8 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: 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 pi-Stacking: E:Y.308 ADP.10: 19 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: PO4.11, MG.12 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:D.159, G:D.159, G:R.212, G:K.215, G:E.216, G:G.304, G:T.305, G:K.338 Salt bridges: G:K.20, G:K.20

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain B: G.15, S.16, Q.139, D.159, G.160, V.161 Ligands: ADP.1, MG.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.16, B:Q.139, B:V.161 PO4.7: 7 residues within 4Å: Chain E: G.15, S.16, Q.139, D.159, V.161 Ligands: ADP.6, MG.8 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.16, E:Q.139, E:V.161 PO4.11: 8 residues within 4Å: Chain G: S.16, G.76, Q.139, D.159, G.160, V.161 Ligands: ADP.10, MG.12 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.16, G:G.76, G:Q.139, G:V.161

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: Q.139 Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain E: Q.139 Ligands: ADP.6, PO4.7 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain G: Q.139 Ligands: ADP.10, PO4.11 No protein-ligand interaction detected (PLIP)

3 x 9UE: Jasplakinolide(Non-covalent)(Covalent)

9UE.4: 17 residues within 4Å: Chain B: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 Chain E: H.75, I.77, L.112, P.114, A.116, R.179, D.181 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:T.196, B:Y.200, B:Y.200, B:F.202, B:L.244, E:I.77, E:P.114 Hydrogen bonds: B:G.199, B:S.201 9UE.5: 8 residues within 4Å: Chain B: I.289 Chain G: H.75, I.77, L.112, P.114, A.116, R.179, D.181 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:I.289, G:I.77, G:I.77, G:P.114 9UE.9: 18 residues within 4Å: Chain B: H.75, I.77, L.112, P.114, A.116, R.179, D.181 Chain E: I.289 Chain G: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain B Hydrophobic interactions: G:T.196, G:Y.200, G:Y.200, G:F.202, G:L.244, B:I.77, B:P.114 Hydrogen bonds: G:G.199, G:S.201

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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