SMTL ID : 8uxx.1

Arp2/3 branch junction complex, BeFx state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-8-mer

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: D.11, G.13, T.14, G.15, Y.16, K.18, G.187, D.188, G.189, G.213, R.214, E.238, K.241, E.242, G.334, G.335, S.336, L.338, F.339, R.383 Ligands: MG.2, BEF.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.14, A:G.15, A:Y.16, A:Y.16, A:D.188, A:D.188, A:G.189, A:K.241, A:E.242, A:G.335 Water bridges: A:K.18, A:K.18, A:Q.160 Salt bridges: A:K.18, A:K.18, A:R.383 pi-Stacking: A:F.339 ADP.7: 20 residues within 4Å: Chain H: D.13, G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:G.15, H:S.16, H:S.16, H:G.17, H:L.18, H:D.159, H:D.159, H:G.184, H:K.215, H:G.304, H:K.338 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308 ADP.9: 20 residues within 4Å: Chain I: D.13, G.15, S.16, L.18, K.20, Q.139, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:S.16, I:L.18, I:D.159, I:D.159, I:D.159, I:K.215, I:E.216, I:G.304, I:K.338 Salt bridges: I:K.20, I:K.20 pi-Stacking: I:Y.308 ADP.10: 20 residues within 4Å: Chain J: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.11, BEF.12 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:S.16, J:G.17, J:L.18, J:D.159, J:K.215, J:E.216, J:E.216, J:G.304, J:T.305, J:M.307, J:K.338 Salt bridges: J:K.20, J:K.20 pi-Stacking: J:Y.308 ADP.13: 22 residues within 4Å: Chain K: D.13, G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.14, BEF.15 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.15, K:S.16, K:G.17, K:L.18, K:D.159, K:D.159, K:K.215, K:E.216, K:E.216, K:G.304, K:K.338 Salt bridges: K:K.20, K:K.20 pi-Stacking: K:Y.308 ADP.16: 21 residues within 4Å: Chain L: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.17, BEF.18 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:S.16, L:S.16, L:G.17, L:L.18, L:D.159, L:D.159, L:D.159, L:K.215, L:E.216, L:E.216, L:E.216, L:G.304 Salt bridges: L:K.20, L:K.20 ADP.19: 22 residues within 4Å: Chain M: D.13, G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.20, BEF.21 13 PLIP interactions: 13 interactions with chain M Hydrogen bonds: M:G.15, M:S.16, M:G.17, M:L.18, M:D.159, M:D.159, M:K.215, M:E.216, M:G.304, M:K.338 Salt bridges: M:K.20, M:K.20 pi-Stacking: M:Y.308 ADP.22: 22 residues within 4Å: Chain N: D.13, G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.23, BEF.24 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:S.16, N:G.17, N:L.18, N:D.159, N:D.159, N:D.159, N:K.215, N:E.216, N:E.216, N:G.304, N:K.338 Salt bridges: N:K.20, N:K.20 ADP.25: 22 residues within 4Å: Chain O: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.26, BEF.27 16 PLIP interactions: 16 interactions with chain O Hydrogen bonds: O:S.16, O:S.16, O:S.16, O:G.17, O:L.18, O:D.159, O:D.159, O:G.160, O:K.215, O:E.216, O:E.216, O:G.304, O:K.338 Salt bridges: O:K.20, O:K.20 pi-Stacking: O:Y.308

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.11, G.13, K.18, Q.160, G.187 Ligands: ADP.1, BEF.3 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain B: D.9, K.16, Q.137, D.154, G.156, V.350 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain H: G.15, S.16, K.20, Q.139, G.158, D.159 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain I: D.13, G.15, K.20, Q.139, V.341 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.13 MG.11: 8 residues within 4Å: Chain J: G.15, S.16, K.20, Q.139, G.158, D.159 Ligands: ADP.10, BEF.12 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain K: G.15, S.16, K.20, Q.139, G.158 Ligands: ADP.13, BEF.15 No protein-ligand interaction detected (PLIP) MG.17: 7 residues within 4Å: Chain L: G.15, K.20, Q.139, D.156, G.158 Ligands: ADP.16, BEF.18 No protein-ligand interaction detected (PLIP) MG.20: 7 residues within 4Å: Chain M: D.13, G.15, K.20, Q.139, G.158 Ligands: ADP.19, BEF.21 No protein-ligand interaction detected (PLIP) MG.23: 8 residues within 4Å: Chain N: D.13, G.15, S.16, K.20, Q.139, G.158 Ligands: ADP.22, BEF.24 No protein-ligand interaction detected (PLIP) MG.26: 7 residues within 4Å: Chain O: D.13, G.15, K.20, Q.139, G.158 Ligands: ADP.25, BEF.27 No protein-ligand interaction detected (PLIP)

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

BEF.3: 11 residues within 4Å: Chain A: G.13, T.14, G.15, G.97, Q.160, G.187, D.188, G.189, V.190 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) BEF.12: 10 residues within 4Å: Chain J: G.15, S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain K: G.15, S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) BEF.18: 11 residues within 4Å: Chain L: G.15, S.16, G.17, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP) BEF.21: 10 residues within 4Å: Chain M: G.15, S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.19, MG.20 No protein-ligand interaction detected (PLIP) BEF.24: 9 residues within 4Å: Chain N: G.15, S.16, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.22, MG.23 No protein-ligand interaction detected (PLIP) BEF.27: 10 residues within 4Å: Chain O: G.15, S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP)

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

ATP.5: 26 residues within 4Å: Chain B: D.9, G.11, T.12, G.13, F.14, K.16, G.74, Q.137, G.156, D.157, G.158, V.159, G.182, R.183, R.210, K.213, E.214, C.217, G.301, G.302, S.303, M.305, Y.306, R.347 Chain C: D.55 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.12, B:T.12, B:G.13, B:F.14, B:D.157, B:D.157, B:D.157, B:G.158, B:V.159, B:K.213, B:E.214, B:E.214, B:E.214, B:G.302, B:R.347 Salt bridges: B:K.16, B:K.16 pi-Stacking: B:Y.306

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-related protein 3: A
Actin-related protein 2: B
Actin-related protein 2/3 complex subunit 1: C
Actin-related protein 2/3 complex subunit 2: D
Actin-related protein 2/3 complex subunit 3: E
Actin-related protein 2/3 complex subunit 4: F
Actin-related protein 2/3 complex subunit 5: G
Actin, alpha skeletal muscle: HIJKLMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
M

K
N

L
O

M
P

N
Q

O
R

Actin-related protein 3

Actin-related protein 2

Actin-related protein 2/3 complex subunit 1

Actin-related protein 2/3 complex subunit 2

Actin-related protein 2/3 complex subunit 3

Actin-related protein 2/3 complex subunit 4

Actin-related protein 2/3 complex subunit 5

Actin, alpha skeletal muscle

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