SMTL ID : 8uz1.1

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

Coordinates

PDB Format Compare

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: 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, BEF.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.11, A:D.154, 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 pi-Stacking: A:Y.303 ADP.4: 22 residues within 4Å: Chain B: 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.5, BEF.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.11, B:D.154, B:D.154, B:K.210, B:E.211, B:E.211, B:G.299, B:K.333 Salt bridges: B:K.15, B:K.15 ADP.7: 21 residues within 4Å: Chain C: 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.8, BEF.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.11, C:D.154, C:D.154, C:K.210, C:E.211, C:E.211, C:G.299, C:K.333 Salt bridges: C:K.15, C:K.15 ADP.10: 22 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.11, BEF.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.11, D:D.154, D:D.154, D:K.210, D:E.211, D:E.211, D:G.299, D:K.333 Salt bridges: D:K.15, D:K.15 ADP.13: 22 residues within 4Å: Chain E: 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.14, BEF.15 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.11, E:D.154, E:D.154, E:K.210, E:E.211, E:E.211, E:G.299, E:K.333 Salt bridges: E:K.15, E:K.15 ADP.16: 22 residues within 4Å: Chain F: 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.17, BEF.18 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.11, F:D.154, F:D.154, F:K.210, F:E.211, F:E.211, F:G.299, F:K.333 Salt bridges: F:K.15, F:K.15 ADP.19: 21 residues within 4Å: Chain G: 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.20, BEF.21 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.11, G:D.154, G:D.154, G:K.210, G:E.211, G:E.211, G:G.299, G:K.333 Salt bridges: G:K.15, G:K.15 ADP.22: 22 residues within 4Å: Chain H: 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.23, BEF.24 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:S.11, H:D.154, H:D.154, H:K.210, H:E.211, H:E.211, H:G.299, H:K.333 Salt bridges: H:K.15, H:K.15 ADP.25: 21 residues within 4Å: Chain I: 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.26, BEF.27 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:S.11, I:D.154, I:D.154, I:K.210, I:E.211, I:E.211, I:G.299, I:K.333 Salt bridges: I:K.15, I:K.15

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: Q.134, D.151, G.153, V.336 Ligands: ADP.1, BEF.3 No protein-ligand interaction detected (PLIP) MG.5: 6 residues within 4Å: Chain B: Q.134, D.151, G.153, V.336 Ligands: ADP.4, BEF.6 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain C: G.10, Q.134, G.153, V.336 Ligands: ADP.7, BEF.9 No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain D: Q.134, D.151, G.153, V.336 Ligands: ADP.10, BEF.12 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain E: G.10, Q.134, G.153, V.336 Ligands: ADP.13, BEF.15 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain F: Q.134, G.153, V.336 Ligands: ADP.16, BEF.18 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain G: Q.134, G.153, V.336 Ligands: ADP.19, BEF.21 No protein-ligand interaction detected (PLIP) MG.23: 6 residues within 4Å: Chain H: Q.134, D.151, G.153, V.336 Ligands: ADP.22, BEF.24 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain I: Q.134, G.153 Ligands: ADP.25, BEF.27 No protein-ligand interaction detected (PLIP)

9 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 10 residues within 4Å: Chain A: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.6: 10 residues within 4Å: Chain B: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) BEF.9: 10 residues within 4Å: Chain C: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.12: 10 residues within 4Å: Chain D: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain E: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 10 residues within 4Å: Chain F: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP) BEF.21: 10 residues within 4Å: Chain G: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.19, MG.20 No protein-ligand interaction detected (PLIP) BEF.24: 10 residues within 4Å: Chain H: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.22, MG.23 No protein-ligand interaction detected (PLIP) BEF.27: 10 residues within 4Å: Chain I: G.10, S.11, G.71, Q.134, G.153, D.154, G.155, V.156 Ligands: ADP.25, MG.26 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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