SMTL ID : 8uxw.1

Arp2/3 branch junction complex, ADP 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: 20 residues within 4Å: Chain A: 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 15 PLIP interactions: 15 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:K.241, A:E.242, A:E.242, A:G.335, A:S.336 Salt bridges: A:K.18, A:K.18, A:R.383 pi-Stacking: A:F.339 ADP.6: 21 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, P.309, K.338 Ligands: MG.5 15 PLIP interactions: 15 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:K.215, H:E.216, H:E.216, H:G.304, H:K.338 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308 ADP.8: 21 residues within 4Å: Chain I: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, G.158, D.159, G.184, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.7 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.15, I:S.16, I:G.17, I:L.18, I:D.159, I:D.159, I:D.159, I:K.215, I:E.216, I:G.304, I:T.305, 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.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:S.16, J:G.17, J:L.18, J:D.159, J:D.159, J:K.215, J:E.216, J:E.216, J:E.216, J:G.304, J:T.305 Salt bridges: J:K.20, J:K.20 pi-Stacking: J:Y.308 ADP.12: 19 residues within 4Å: Chain K: 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 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:G.304, K:T.305, K:K.338 Salt bridges: K:K.20, K:K.20 pi-Stacking: K:Y.308 ADP.14: 20 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.13 15 PLIP interactions: 15 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 pi-Stacking: L:Y.308 ADP.16: 21 residues within 4Å: Chain M: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.185, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.15 11 PLIP interactions: 11 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:G.304, M:T.305 Salt bridges: M:K.20, M:K.20 ADP.18: 20 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.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.17 15 PLIP interactions: 15 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:D.159, N:G.160, N:K.215, N:E.216, N:G.304, N:K.338 Salt bridges: N:K.20, N:K.20 pi-Stacking: N:Y.308 ADP.20: 19 residues within 4Å: Chain O: 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.19 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:S.16, O:G.17, O:L.18, O:D.159, O:D.159, O:D.159, O:K.215, O:E.216, O:G.304, O:T.305, 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: 6 residues within 4Å: Chain A: G.13, T.14, K.18, G.187, D.188 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain B: K.16, D.154, G.156, V.350 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain H: G.15, S.16, K.20, Q.139, G.158, D.159 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain I: D.13, G.15, S.16, K.20, Q.139 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.13 MG.9: 7 residues within 4Å: Chain J: G.15, S.16, K.20, Q.139, G.158, D.159 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.11: 7 residues within 4Å: Chain K: G.15, S.16, K.20, Q.139, G.158, D.159 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain L: G.15, S.16, K.20, G.158, D.159 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain M: G.15, S.16, K.20, G.158, D.159 Ligands: ADP.16 No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain N: D.13, G.15, K.20, Q.139, V.341 Ligands: ADP.18 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.13 MG.19: 7 residues within 4Å: Chain O: G.15, S.16, K.20, Q.139, G.158, D.159 Ligands: ADP.20 No protein-ligand interaction detected (PLIP)

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

ATP.4: 25 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 Ligands: MG.3 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:V.159, B:K.213, B:E.214, B:E.214, B:E.214, B:G.302 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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