SMTL ID : 5ood.1

Cryo-EM structure of jasplakinolide-stabilized F-actin in complex with ADP-Pi

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, Y.306 Ligands: PO4.2, MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.157, A:D.157, A:K.213, A:E.214, A:E.214, A:G.302 Salt bridges: A:K.18 pi-Stacking: A:Y.306 ADP.6: 15 residues within 4Å: Chain B: S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, Y.306 Ligands: PO4.7, MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.157, B:D.157, B:K.213, B:E.214, B:E.214, B:G.302 Salt bridges: B:K.18 pi-Stacking: B:Y.306 ADP.10: 15 residues within 4Å: Chain C: S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, Y.306 Ligands: PO4.11, MG.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.157, C:D.157, C:K.213, C:E.214, C:E.214, C:G.302 Salt bridges: C:K.18 pi-Stacking: C:Y.306 ADP.14: 15 residues within 4Å: Chain D: S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, Y.306 Ligands: PO4.15, MG.16 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.157, D:D.157, D:K.213, D:E.214, D:E.214, D:G.302 Salt bridges: D:K.18 pi-Stacking: D:Y.306 ADP.18: 15 residues within 4Å: Chain E: S.14, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.302, T.303, M.305, Y.306 Ligands: PO4.19, MG.20 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.157, E:D.157, E:K.213, E:E.214, E:E.214, E:G.302 Salt bridges: E:K.18 pi-Stacking: E:Y.306

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

PO4.2: 7 residues within 4Å: Chain A: G.13, S.14, Q.137, G.158, V.159 Ligands: ADP.1, MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.14, A:Q.137, A:G.158, A:V.159 PO4.7: 7 residues within 4Å: Chain B: G.13, S.14, Q.137, G.158, V.159 Ligands: ADP.6, MG.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.14, B:Q.137, B:G.158, B:V.159 PO4.11: 7 residues within 4Å: Chain C: G.13, S.14, Q.137, G.158, V.159 Ligands: ADP.10, MG.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.14, C:Q.137, C:G.158, C:V.159 PO4.15: 7 residues within 4Å: Chain D: G.13, S.14, Q.137, G.158, V.159 Ligands: ADP.14, MG.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.14, D:Q.137, D:G.158, D:V.159 PO4.19: 7 residues within 4Å: Chain E: G.13, S.14, Q.137, G.158, V.159 Ligands: ADP.18, MG.20 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.14, E:Q.137, E:G.158, E:V.159

5 x 9ZK: (4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-10-(4-azanylbutyl)-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-1-oxa-5,8,11-triazacyclononadec-15-ene-2,6,9,12-tetrone(Non-covalent)

9ZK.3: 5 residues within 4Å: Chain A: I.75, P.112, A.114, R.177, D.179 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.75, A:P.112 9ZK.5: 13 residues within 4Å: Chain A: G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain B: I.75, P.112, A.114, R.177, D.179 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.198, A:F.200, A:L.242, A:Q.246, B:I.75, B:P.112 Hydrogen bonds: A:G.197 9ZK.9: 13 residues within 4Å: Chain B: G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain C: I.75, P.112, A.114, R.177, D.179 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.75, C:P.112, B:Y.198, B:F.200, B:L.242, B:Q.246 Hydrogen bonds: B:G.197 9ZK.13: 13 residues within 4Å: Chain C: G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain D: I.75, P.112, A.114, R.177, D.179 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.198, C:F.200, C:L.242, C:Q.246, D:I.75, D:P.112 Hydrogen bonds: C:G.197 9ZK.17: 13 residues within 4Å: Chain D: G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain E: I.75, P.112, A.114, R.177, D.179 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.198, D:F.200, D:L.242, D:Q.246, E:I.75, E:P.112 Hydrogen bonds: D:G.197

5 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.154 Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: D.154 Ligands: ADP.6, PO4.7 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: D.154 Ligands: ADP.10, PO4.11 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: D.154 Ligands: ADP.14, PO4.15 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain E: D.154 Ligands: ADP.18, PO4.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merino, F. et al., Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-06-13

Peptides

Actin, alpha skeletal muscle: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Actin, alpha skeletal muscle

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