SMTL ID : 7t5q.1

Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

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

ATP.2: 15 residues within 4Å: Chain A: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, G.173, K.228, E.229, G.324, S.325, M.327, R.374 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.14, A:T.14, A:G.15, A:Y.16, A:Y.16, A:D.172, A:D.172, A:D.172, A:G.173, A:K.228, A:G.324 Salt bridges: A:K.18, A:K.18, A:R.374 ATP.4: 17 residues within 4Å: Chain B: G.14, T.15, F.17, K.19, G.160, D.161, G.162, R.214, K.217, E.218, G.305, G.306, S.307, M.309, Y.310, K.351 Ligands: MG.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.15, B:D.161, B:D.161, B:G.162, B:R.214, B:K.217, B:G.306, B:M.309 Salt bridges: B:K.19, B:K.19

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

ADP.5: 16 residues within 4Å: Chain H: G.13, S.14, G.15, L.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:S.14, H:G.15, H:L.16, H:D.157, H:D.157, H:D.157, H:R.210, H:K.213, H:G.302 Salt bridges: H:K.18, H:K.18, H:K.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Eeuwen, T. et al., Transition State of Arp2/3 Complex Activation by Actin-Bound Dimeric Nucleation-Promoting Factor. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-06-14

Peptides

Actin-related protein 3: A
Actin-related protein 2: B
Actin-related protein 2/3 complex subunit 1A: 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: H
F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera: I
F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera: J

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
J

Actin-related protein 3

Actin-related protein 2

Actin-related protein 2/3 complex subunit 1A

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

F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera

F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera

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