SMTL ID : 8f8t.1

Cryo-EM structure of the Tropomodulin-capped pointed end of F-actin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: G.15, S.16, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.16, A:L.18, A:D.159, A:K.215, A:E.216, A:G.304 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.3: 16 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.16, 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:K.338 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.5: 17 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 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:K.338 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308 ADP.7: 15 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.17, D:L.18, D:D.159, D:D.159, D:D.159, D:K.215, D:E.216, D:G.304, D:K.338 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.9: 17 residues within 4Å: Chain E: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.17, E:L.18, E:D.159, E:D.159, E:D.159, E:K.215, E:E.216, E:G.304, E:K.338 Salt bridges: E:K.20, E:K.20 pi-Stacking: E:Y.308 ADP.11: 17 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.17, F:L.18, F:D.159, F:D.159, F:D.159, F:K.215, F:G.304, F:M.307, F:K.338 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308 ADP.13: 15 residues within 4Å: Chain G: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:G.17, G:L.18, G:D.159, G:D.159, G:D.159, G:K.215, G:E.216, G:G.304, G:K.338 Salt bridges: G:K.20, G:K.20 pi-Stacking: G:Y.308

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.13, K.20 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.13 MG.4: 2 residues within 4Å: Chain B: Q.139 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: Q.139 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.139, D.156 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: Q.139 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: Q.139 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain G: G.158 Ligands: ADP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carman, P.J. et al., Structures of the free and capped ends of the actin filament. Science (2023)

Release Date

2023-06-07

Peptides

Actin, alpha skeletal muscle: ABCDEFG
Tropomodulin-1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
T

Actin, alpha skeletal muscle

Tropomodulin-1

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