SMTL ID : 9m5e.1

Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-2-3-mer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain I: D.156, V.341 Ligands: ADP.6 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.156, I:D.156 MG.7: 3 residues within 4Å: Chain J: D.13, Q.139 Ligands: ADP.8 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.13, J:D.13

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

ADP.2: 15 residues within 4Å: Chain A: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, G.197, K.228, E.229, G.324, S.325, F.328, R.374 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.15, A:Y.16, A:D.172, A:D.172, A:D.172, A:K.228, A:E.229, A:G.324, A:R.374 Salt bridges: A:K.18, A:K.18 ADP.4: 18 residues within 4Å: Chain B: G.14, T.15, G.16, F.17, K.19, G.160, D.161, G.186, R.214, K.217, E.218, G.305, G.306, S.307, M.309, Y.310 Chain C: N.52 Ligands: MG.3 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.15, B:G.16, B:F.17, B:F.17, B:D.161, B:D.161, B:D.161, B:K.217, B:G.306, C:N.52, C:N.52 Salt bridges: B:K.19, B:K.19 ADP.6: 16 residues within 4Å: Chain I: D.13, S.16, G.17, L.18, K.20, D.156, G.158, D.159, R.212, K.215, E.216, G.304, T.305, M.307, K.338 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:D.13, I:L.18, I:D.159, I:D.159, I:K.215, I:E.216, I:E.216, I:G.304 Salt bridges: I:K.20, I:K.20 ADP.8: 16 residues within 4Å: Chain J: D.13, G.15, S.16, L.18, K.20, Q.139, G.158, D.159, K.215, E.216, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:L.18, J:L.18, J:Q.139, J:D.159, J:D.159, J:D.159, J:K.215, J:G.304 Salt bridges: J:K.20, J:K.20 pi-Stacking: J:Y.308 ADP.9: 15 residues within 4Å: Chain K: G.15, S.16, L.18, K.20, G.158, D.159, G.184, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:S.16, K:D.159, K:D.159, K:K.215, K:E.216, K:G.304 Salt bridges: K:K.20, K:K.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Francis, J. et al., Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-09-10

Peptides

Actin-related protein 3: A
Actin-related protein 2: B
Actin-related protein 2/3 complex subunit 1B: 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
NCK-interacting protein with SH3 domain: HL
Actin, alpha skeletal muscle: IJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

L
h

I
I

J
J

K
K

Actin-related protein 3

Actin-related protein 2

Actin-related protein 2/3 complex subunit 1B

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

NCK-interacting protein with SH3 domain

Actin, alpha skeletal muscle

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