SMTL ID : 6w17.1

Structure of Dip1-activated Arp2/3 complex with nucleated actin filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-4-mer

Ligands

5 x HYP- ALA- TRP- G5G- ALA- ALO- CYS: Phalloidin(Non-covalent)

HYP-ALA-TRP-G5G-ALA-ALO-CYS.1: 13 residues within 4Å: Chain A: L.364 Chain B: E.72, I.75, R.77, R.177, D.179 Chain I: T.196, G.199, Y.200, S.201, F.202, E.207, Q.248 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain I Hydrophobic interactions: B:I.75, I:T.196, I:Y.200, I:F.202 Hydrogen bonds: I:Q.248 HYP-ALA-TRP-G5G-ALA-ALO-CYS.2: 13 residues within 4Å: Chain B: V.287, R.290 Chain I: H.75, I.77, R.179, D.181 Chain J: T.196, G.199, Y.200, S.201, F.202, E.207, Q.248 9 PLIP interactions: 6 interactions with chain J, 3 interactions with chain B Hydrophobic interactions: J:T.196, J:Y.200, J:F.202, B:V.287 Hydrogen bonds: J:S.201, J:S.201, J:Q.248, B:R.290, B:R.290 HYP-ALA-TRP-G5G-ALA-ALO-CYS.3: 9 residues within 4Å: Chain J: H.75, I.77, R.179, D.181 Chain K: T.196, G.199, Y.200, S.201, Q.248 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: K:T.196, K:Y.200, J:I.77 Hydrogen bonds: K:Q.248 HYP-ALA-TRP-G5G-ALA-ALO-CYS.4: 13 residues within 4Å: Chain K: E.74, H.75, I.77, T.79, R.179, D.181 Chain L: T.196, G.199, Y.200, S.201, F.202, E.207, Q.248 7 PLIP interactions: 4 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:T.196, L:Y.200, L:F.202, K:I.77, K:I.77, K:T.79 Hydrogen bonds: L:Q.248 HYP-ALA-TRP-G5G-ALA-ALO-CYS.5: 7 residues within 4Å: Chain K: I.289 Chain L: E.74, H.75, I.77, T.79, R.179, D.181 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:I.289, L:I.77, L:T.79 Hydrogen bonds: L:E.74

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: Q.160 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: Q.137, D.154 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain I: Q.139, D.156, G.158 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain J: Q.139, D.156, G.158 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain K: G.158 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain L: Q.139, G.158 Ligands: ADP.16 No protein-ligand interaction detected (PLIP)

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

ATP.7: 15 residues within 4Å: Chain A: N.12, G.13, T.14, G.15, Y.16, K.18, G.187, D.188, K.241, E.242, G.335, S.336, L.338, F.339 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.14, A:G.15, A:Y.16, A:Q.160, A:D.188, A:D.188, A:D.188, A:G.335, A:L.338 Salt bridges: A:K.18, A:K.18, A:K.18 pi-Stacking: A:F.339 ATP.9: 16 residues within 4Å: Chain B: G.11, T.12, F.14, K.16, Q.137, G.156, D.157, R.210, K.213, E.214, G.302, S.303, M.305, Y.306, R.347 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.12, B:T.12, B:G.13, B:F.14, B:Q.137, B:D.157, B:D.157, B:K.213, B:R.347 Salt bridges: B:K.16, B:K.16, B:R.347

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

ADP.10: 18 residues within 4Å: Chain I: D.13, G.15, S.16, L.18, K.20, Q.139, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:D.13, I:G.15, I:S.16, I:D.159, I:D.159, I:K.215, I:G.304, I:T.305, I:K.338 Salt bridges: I:K.20, I:K.20 pi-Stacking: I:Y.308 ADP.12: 17 residues within 4Å: Chain J: D.13, G.15, S.16, L.18, K.20, Q.139, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:D.13, J:S.16, J:D.159, J:D.159, J:K.215, J:E.216, J:G.304 Salt bridges: J:K.20, J:K.20 ADP.14: 17 residues within 4Å: Chain K: D.13, G.15, S.16, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.15 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:D.13, K:S.16, K:D.159, K:D.159, K:K.215, K:G.304 Salt bridges: K:K.20, K:K.20 ADP.16: 15 residues within 4Å: Chain L: G.15, K.20, Q.139, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.17 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:S.16, L:Q.139, L:D.159, L:D.159, L:R.212, L:K.215, L:G.304 Salt bridges: L:K.20, L:K.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaaban, M. et al., Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-08-12

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
Protein dip1: H
Actin, alpha skeletal muscle: IJKL

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

K
K

L
L

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

Protein dip1

Actin, alpha skeletal muscle

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