SMTL ID : 5ooc.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:L.16, A:D.157, A:R.210, A:K.213, A:E.214, A:G.302, A:K.336 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306 ADP.5: 18 residues within 4Å: Chain B: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:L.16, B:D.157, B:R.210, B:K.213, B:E.214, B:G.302, B:K.336 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306 ADP.8: 18 residues within 4Å: Chain C: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.14, C:G.15, C:L.16, C:D.157, C:R.210, C:K.213, C:E.214, C:G.302, C:K.336 Salt bridges: C:K.18, C:K.18 pi-Stacking: C:Y.306 ADP.11: 18 residues within 4Å: Chain D: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.14, D:G.15, D:L.16, D:D.157, D:R.210, D:K.213, D:E.214, D:G.302, D:K.336 Salt bridges: D:K.18, D:K.18 pi-Stacking: D:Y.306 ADP.14: 18 residues within 4Å: Chain E: G.13, S.14, G.15, L.16, K.18, S.155, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.14, E:G.15, E:L.16, E:D.157, E:R.210, E:K.213, E:E.214, E:G.302, E:K.336 Salt bridges: E:K.18, E:K.18 pi-Stacking: E:Y.306

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.2: 4 residues within 4Å: Chain A: I.75, P.112, A.114, D.179 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.75, A:I.75, A:P.112 9ZK.4: 13 residues within 4Å: Chain A: R.196, G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain B: I.75, P.112, A.114, D.179 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.75, B:I.75, B:P.112, A:F.200, A:V.201, A:L.242 Hydrogen bonds: A:S.199, A:E.205 9ZK.7: 13 residues within 4Å: Chain B: R.196, G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain C: I.75, P.112, A.114, D.179 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.200, B:V.201, B:L.242, C:I.75, C:I.75, C:P.112 Hydrogen bonds: B:S.199, B:E.205 9ZK.10: 13 residues within 4Å: Chain C: R.196, G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain D: I.75, P.112, A.114, D.179 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.200, C:V.201, C:L.242, D:I.75, D:I.75, D:P.112 Hydrogen bonds: C:S.199, C:E.205 9ZK.13: 13 residues within 4Å: Chain D: R.196, G.197, Y.198, S.199, F.200, V.201, E.205, L.242, Q.246 Chain E: I.75, P.112, A.114, D.179 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.200, D:V.201, D:L.242, E:I.75, E:I.75, E:P.112 Hydrogen bonds: D:S.199, D:E.205

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.11, D.154 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: D.11, D.154 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: D.11, D.154 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain D: D.11, D.154 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain E: D.11, D.154 Ligands: ADP.14 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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