SMTL ID : 8f8q.1

Cryo-EM structure of the CapZ-capped barbed end of F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-mer

Ligands

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

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

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: Q.139 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.139 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: K.20, Q.139 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain D: D.13, K.20, Q.139 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: D.13, Q.139 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: ADP.11 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: ABCDEF
F-actin-capping protein subunit alpha-1: G
F-actin-capping protein subunit beta: H

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

F-actin-capping protein subunit alpha-1

F-actin-capping protein subunit beta

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