SMTL ID : 8uz0.1

Straight actin filament from Arp2/3 branch junction sample (ADP)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-9-mer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: D.8, G.10, S.11, L.13, K.15, Q.134, G.153, D.154, G.155, G.179, R.180, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.11, A:L.13, A:D.154, A:D.154, A:K.210, A:E.211, A:E.211, A:E.211, A:G.299, A:K.333 Salt bridges: A:K.15, A:K.15 ADP.3: 18 residues within 4Å: Chain B: G.10, S.11, L.13, K.15, G.153, D.154, G.155, G.179, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.11, B:L.13, B:D.154, B:D.154, B:G.155, B:K.210, B:E.211, B:E.211, B:E.211, B:G.299, B:T.300, B:K.333 Salt bridges: B:K.15, B:K.15 pi-Stacking: B:Y.303 ADP.5: 18 residues within 4Å: Chain C: G.10, S.11, L.13, K.15, G.153, D.154, G.155, G.179, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.11, C:L.13, C:D.154, C:D.154, C:D.154, C:G.155, C:K.210, C:E.211, C:E.211, C:E.211, C:G.299, C:K.333 Salt bridges: C:K.15, C:K.15 pi-Stacking: C:Y.303 ADP.7: 21 residues within 4Å: Chain D: G.10, S.11, G.12, L.13, K.15, Q.134, G.153, D.154, G.155, G.179, R.180, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.11, D:L.13, D:D.154, D:D.154, D:D.154, D:G.155, D:K.210, D:E.211, D:E.211, D:E.211, D:G.299, D:K.333 Salt bridges: D:K.15, D:K.15 pi-Stacking: D:Y.303 ADP.9: 19 residues within 4Å: Chain E: G.10, S.11, L.13, K.15, G.153, D.154, G.155, G.179, R.180, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.11, E:L.13, E:D.154, E:D.154, E:D.154, E:K.210, E:E.211, E:E.211, E:E.211, E:G.299, E:K.333 Salt bridges: E:K.15, E:K.15 pi-Stacking: E:Y.303 ADP.11: 18 residues within 4Å: Chain F: G.10, S.11, L.13, K.15, G.153, D.154, G.155, G.179, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.11, F:L.13, F:D.154, F:D.154, F:D.154, F:K.210, F:E.211, F:E.211, F:E.211, F:G.299, F:K.333 Salt bridges: F:K.15, F:K.15 pi-Stacking: F:Y.303 ADP.13: 20 residues within 4Å: Chain G: G.10, S.11, G.12, L.13, K.15, G.153, D.154, G.155, G.179, R.180, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.14 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.11, G:L.13, G:D.154, G:D.154, G:K.210, G:E.211, G:E.211, G:E.211, G:G.299, G:K.333 Salt bridges: G:K.15, G:K.15 pi-Stacking: G:Y.303 ADP.15: 19 residues within 4Å: Chain H: G.10, S.11, G.12, L.13, K.15, G.153, D.154, G.155, G.179, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:S.11, H:L.13, H:Q.134, H:D.154, H:D.154, H:G.155, H:K.210, H:E.211, H:E.211, H:E.211, H:G.299, H:K.333 Salt bridges: H:K.15, H:K.15 pi-Stacking: H:Y.303 ADP.17: 21 residues within 4Å: Chain I: D.8, G.10, S.11, G.12, L.13, K.15, Q.134, G.153, D.154, G.155, G.179, R.207, K.210, E.211, G.298, G.299, T.300, M.302, Y.303, K.333 Ligands: MG.18 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:S.11, I:L.13, I:D.154, I:D.154, I:K.210, I:E.211, I:E.211, I:E.211, I:G.299, I:K.333 Salt bridges: I:K.15, I:K.15 pi-Stacking: I:Y.303

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.8, K.15, Q.134, D.151, G.153, V.336 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain B: Q.134, D.151, G.153, V.336 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain C: G.10, K.15, Q.134, G.153 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 7 residues within 4Å: Chain D: G.10, K.15, Q.134, D.151, G.153, V.336 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain E: K.15, Q.134, G.153, V.336 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain F: K.15, Q.134, G.153, V.336 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain G: G.10, K.15, Q.134, D.151, G.153, V.336 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain H: Q.134, G.153, V.336 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain I: D.8, Q.134, D.151, G.153, V.336 Ligands: ADP.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chavali, S.S. et al., Cryo-EM structures reveal how phosphate release from Arp3 weakens actin filament branches formed by Arp2/3 complex. Nat Commun (2024)

Release Date

2024-01-31

Peptides

Actin, alpha skeletal muscle: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

D
M

E
N

F
O

G
P

H
Q

I
R

Actin, alpha skeletal muscle

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