SMTL ID : 8vkh.1

Structure of gelsolin domains G1-G3 bound to the barbed end of F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:L.16, A:D.157, A:D.157, A:K.213, A:E.214, A:G.302, A:T.303 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306 ADP.3: 18 residues within 4Å: Chain B: D.11, G.13, S.14, G.15, L.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.13, B:G.15, B:L.16, B:D.157, B:D.157, B:K.213, B:E.214, B:E.214, B:G.302 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306 ADP.5: 15 residues within 4Å: Chain C: G.13, S.14, G.15, L.16, K.18, G.156, D.157, K.213, E.214, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.13, C:S.14, C:G.15, C:L.16, C:D.157, C:D.157, C:D.157, C:K.213, C:E.214, C:G.302 Salt bridges: C:K.18, C:K.18 pi-Stacking: C:Y.306 ADP.7: 16 residues within 4Å: Chain D: G.13, S.14, G.15, L.16, K.18, G.156, D.157, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.13, D:S.14, D:G.15, D:L.16, D:D.157, D:D.157, D:K.213, D:E.214, D:E.214, D:G.302, D:T.303, D:K.336 Salt bridges: D:K.18, D:K.18 pi-Stacking: D:Y.306

14 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) CA.4: 1 residues within 4Å: Ligands: ADP.3 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain C: Q.137, G.156 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain D: Q.137, G.156 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain E: D.11, Q.137 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) CA.12: 3 residues within 4Å: Chain F: Q.137, D.154 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) CA.13: 4 residues within 4Å: Chain G: G.47, D.48, E.79, V.127 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:G.47, G:E.79, G:E.79, G:V.127 CA.14: 6 residues within 4Å: Chain G: K.148, G.168, D.169, E.191, T.239, D.241 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:G.168, G:D.169, G:D.241, G:D.241 CA.15: 4 residues within 4Å: Chain G: E.284, D.285, N.306, E.309 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.284, G:E.309, G:E.309 CA.16: 5 residues within 4Å: Chain F: E.167 Chain G: D.91, G.96, R.97, A.98 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.91, G:G.96, G:A.98 CA.17: 4 residues within 4Å: Chain H: G.47, D.48, E.79, V.127 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:G.47, H:D.48, H:E.79, H:E.79, H:V.127 CA.18: 5 residues within 4Å: Chain H: K.148, G.168, D.169, E.191, D.241 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:G.168, H:D.169, H:D.241, H:D.241 CA.19: 4 residues within 4Å: Chain H: S.259, E.284, D.285, E.309 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.284, H:D.285, H:E.309 CA.20: 5 residues within 4Å: Chain E: E.167 Chain H: D.91, G.96, R.97, A.98 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.91, H:D.91, H:G.96, H:A.98

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.9: 20 residues within 4Å: Chain E: G.13, S.14, G.15, L.16, K.18, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.14, E:S.14, E:G.15, E:L.16, E:G.156, E:D.157, E:D.157, E:G.158, E:V.159, E:K.213, E:E.214, E:G.302 Salt bridges: E:K.18, E:K.18 pi-Stacking: E:Y.306 ATP.11: 19 residues within 4Å: Chain F: G.13, S.14, G.15, L.16, K.18, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: CA.12 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.14, F:S.14, F:G.15, F:L.16, F:G.156, F:D.157, F:D.157, F:G.158, F:V.159, F:K.213, F:E.214, F:E.214, F:G.302 Salt bridges: F:K.18, F:K.18 pi-Stacking: F:Y.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barrie, K.R. et al., Mechanism of Actin Filament Severing and Capping by Gelsolin. Biorxiv (2024)

Release Date

2024-10-16

Peptides

Actin, alpha skeletal muscle: ABCDEF
Gelsolin: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Actin, alpha skeletal muscle

Gelsolin

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