SMTL ID : 9fjy.1

Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 2).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

4 x TRP- EEP- ALA- DTH- CYS- HYP- ALA: Phalloidin

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 3 residues within 4Å: Chain A: H.72, R.176 Chain B: R.289 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.178, B:R.289, B:R.289 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 12 residues within 4Å: Chain A: T.193, G.196, Y.197, S.198, F.199, Q.245 Chain B: E.71, I.74, P.111, R.176 Chain C: V.286, R.289 10 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:T.193, A:Y.197, A:F.199, B:I.74, B:P.111, C:V.286 Hydrogen bonds: A:S.198, A:Q.245, C:R.289, C:R.289 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 12 residues within 4Å: Chain B: T.193, G.196, Y.197, S.198, F.199, Q.245 Chain C: E.71, I.74, P.111, D.178 Chain D: M.282, V.286 10 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: D:V.286, B:T.193, B:Y.197, B:F.199, C:E.71, C:I.74, C:P.111 Hydrogen bonds: D:M.282, B:S.198, B:Q.245 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 11 residues within 4Å: Chain C: T.193, G.196, Y.197, S.198, F.199, E.204, Q.245 Chain D: E.71, P.111, R.176 Chain E: S.39 9 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: D:E.71, D:P.111, C:T.193, C:Y.197, C:F.199 Hydrogen bonds: C:S.198, C:S.198, C:Q.245, E:S.39

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG.5: 4 residues within 4Å: Chain E: N.40, A.41, L.43, M.267 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain F: N.40, A.41, T.42 No protein-ligand interaction detected (PLIP)

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.7: 17 residues within 4Å: Chain A: D.10, G.12, S.13, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.8, PO4.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.156, A:D.156, A:R.209, A:K.212, A:E.213, A:E.213, A:G.301 Salt bridges: A:K.17, A:K.17, A:K.335 ADP.10: 14 residues within 4Å: Chain B: S.13, M.15, G.155, D.156, R.209, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.11, PO4.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.156, B:D.156, B:E.213, B:G.301 Salt bridges: B:K.17, B:K.335 ADP.13: 14 residues within 4Å: Chain C: S.13, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.300, G.301, Y.305, K.335 Ligands: MG.14, PO4.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:M.15, C:D.156, C:D.156, C:R.209, C:K.212, C:E.213, C:E.213, C:G.301 Salt bridges: C:K.17, C:K.17 ADP.16: 16 residues within 4Å: Chain D: D.10, S.13, G.14, M.15, K.17, G.155, D.156, K.212, E.213, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.17, PO4.18 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.10, D:M.15, D:D.156, D:D.156, D:K.212, D:E.213, D:G.301 Salt bridges: D:K.17, D:K.17 pi-Stacking: D:Y.305

8 x MG: MAGNESIUM ION

MG.8: 3 residues within 4Å: Chain A: Q.136 Ligands: ADP.7, PO4.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: Q.136, G.155 Ligands: ADP.10, PO4.12 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain C: Q.136, G.155 Ligands: ADP.13, PO4.15 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain D: Q.136, D.153, G.155 Ligands: ADP.16, PO4.18 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain E: R.31, D.273 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.273 MG.20: 3 residues within 4Å: Chain E: D.194, D.220, A.232 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.194, E:D.220 MG.21: 2 residues within 4Å: Chain F: R.31, D.273 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.273, F:D.273 MG.22: 3 residues within 4Å: Chain F: D.194, D.220, N.230 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.194, F:D.220

4 x PO4: PHOSPHATE ION

PO4.9: 9 residues within 4Å: Chain A: G.12, S.13, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.7, MG.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.13, A:Q.136, A:Q.136, A:D.156, A:G.157, A:V.158 PO4.12: 9 residues within 4Å: Chain B: S.13, Q.136, D.153, G.155, D.156, G.157, V.158 Ligands: ADP.10, MG.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.136, B:D.156, B:G.157, B:V.158 PO4.15: 9 residues within 4Å: Chain C: G.12, S.13, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.13, MG.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.13, C:Q.136, C:G.155, C:D.156, C:G.157, C:V.158 PO4.18: 9 residues within 4Å: Chain D: G.12, S.13, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.16, MG.17 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.13, D:S.13, D:G.73, D:Q.136, D:D.156, D:G.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boiero Sanders, M. et al., Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly. Nat Commun (2024)

Release Date

2024-09-11

Peptides

Actin, cytoplasmic 1, N-terminally processed: ABCD
Deoxyribonuclease-1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Actin, cytoplasmic 1, N-terminally processed

Deoxyribonuclease-1

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