SMTL ID : 7pm3.1

Cryo-EM structure of young JASP-stabilized F-actin (central 3er)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.17, A:L.18, A:D.159, A:D.159, A:D.159, A:K.215, A:E.216, A:G.304, A:T.305, A:K.338 Salt bridges: A:K.20, A:K.20 ADP.5: 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: PO4.6, MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.17, B:L.18, B:D.159, B:D.159, B:D.159, B:K.215, B:E.216, B:G.304, B:T.305, B:K.338 Salt bridges: B:K.20, B:K.20 ADP.9: 19 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: PO4.10, MG.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.17, C:L.18, C:D.159, C:D.159, C:D.159, C:K.215, C:E.216, C:G.304, C:T.305, C:K.338 Salt bridges: C:K.20, C:K.20

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

PO4.2: 9 residues within 4Å: Chain A: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.1, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.139, A:D.159, A:G.160, A:V.161, A:V.161 PO4.6: 8 residues within 4Å: Chain B: G.15, S.16, G.76, Q.139, G.160, V.161 Ligands: ADP.5, MG.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.16, B:Q.139, B:G.160, B:V.161 PO4.10: 7 residues within 4Å: Chain C: G.15, S.16, Q.139, G.160, V.161 Ligands: ADP.9, MG.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.16, C:Q.139, C:G.160, C:V.161

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: Q.139, D.156 Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.139 Ligands: ADP.5, PO4.6 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: Q.139 Ligands: ADP.9, PO4.10 No protein-ligand interaction detected (PLIP)

3 x 9UE: Jasplakinolide(Non-covalent)

9UE.4: 15 residues within 4Å: Chain A: H.75, I.77, L.112, P.114, D.181 Chain B: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.77, A:P.114, B:T.196, B:Y.200, B:F.202, B:L.244 Hydrogen bonds: A:R.179, B:G.199, B:S.201, B:S.201 9UE.8: 17 residues within 4Å: Chain A: I.289 Chain B: H.75, I.77, P.114, A.116, R.179, D.181 Chain C: T.196, R.198, G.199, Y.200, S.201, F.202, E.207, L.244, Q.248, V.249 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.77, B:P.114, C:T.196, C:Y.200, C:F.202, C:L.244 Hydrogen bonds: B:R.179, C:G.199, C:S.201 9UE.12: 7 residues within 4Å: Chain B: I.289 Chain C: H.75, I.77, P.114, A.116, R.179, D.181 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.77, C:P.114 Hydrogen bonds: C:R.179

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

Actin, alpha skeletal muscle: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Actin, alpha skeletal muscle

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