SMTL ID : 9m64.1

Structure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filaments (Doublet Complex)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-8-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, K.228, E.229, G.323, G.324, S.325, F.328, R.374 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.14, A:G.15, A:Y.16, A:Y.16, A:D.172, A:D.172, A:K.228, A:E.229, A:G.324 Salt bridges: A:K.18, A:K.18, A:R.374 pi-Stacking: A:F.328 ADP.3: 19 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, K.351 Chain C: N.52 Ligands: MG.2 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.16, B:F.17, B:D.161, B:D.161, B:D.161, B:K.217, B:G.306, B:K.351, C:N.52, C:N.52 Salt bridges: B:K.19, B:K.19 pi-Stacking: B:Y.310 ADP.5: 16 residues within 4Å: Chain I: D.13, G.15, S.16, L.18, K.20, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:D.159, I:D.159, I:K.215, I:E.216, I:G.304, I:M.307, I:K.338, I:K.338 Salt bridges: I:K.20, I:K.20 ADP.6: 15 residues within 4Å: Chain J: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, E.216, G.303, G.304, M.307, Y.308, K.338 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:G.15, J:S.16, J:G.17, J:L.18, J:D.159, J:R.212, J:G.304, J:T.305, J:M.307, J:K.338, J:K.338 Salt bridges: J:K.20, J:K.20 ADP.9: 17 residues within 4Å: Chain K: D.13, 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 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:S.16, K:D.159, K:D.159, K:D.159, K:K.215, K:G.304 Salt bridges: K:K.20, K:K.20 pi-Stacking: K:Y.308 ADP.10: 10 residues within 4Å: Chain L: G.15, S.16, G.17, L.18, G.158, D.159, E.216, G.304, T.305, Y.308 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:S.16, L:G.17, L:L.18, L:D.159, L:E.216 pi-Stacking: L:Y.308 ADP.12: 16 residues within 4Å: Chain M: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, K.228, E.229, G.323, G.324, S.325, M.327, F.328, R.374 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:T.14, M:G.15, M:Y.16, M:D.172, M:D.172, M:K.228, M:G.324 Salt bridges: M:K.18, M:K.18, M:R.374 pi-Stacking: M:F.328 ADP.14: 18 residues within 4Å: Chain N: 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, K.351 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:G.16, N:F.17, N:D.161, N:D.161, N:D.161, N:K.217, N:G.306 Salt bridges: N:K.19, N:K.19 ADP.15: 18 residues within 4Å: Chain U: D.13, G.15, S.16, G.17, 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 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain U Hydrogen bonds: U:G.15, U:G.17, U:L.18, U:D.159, U:D.159, U:K.215, U:E.216, U:E.216, U:G.304 Salt bridges: U:K.20, U:K.20, U:K.338 pi-Stacking: U:Y.308 ADP.18: 18 residues within 4Å: Chain V: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.17 12 PLIP interactions: 12 interactions with chain V Hydrogen bonds: V:S.16, V:G.17, V:L.18, V:L.18, V:D.159, V:D.159, V:K.215, V:G.304, V:K.338 Salt bridges: V:K.20, V:K.20 pi-Stacking: V:Y.308 ADP.19: 16 residues within 4Å: Chain W: 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 Ligands: MG.20 9 PLIP interactions: 9 interactions with chain W Hydrogen bonds: W:S.16, W:D.159, W:K.215, W:E.216, W:G.304, W:T.305 Salt bridges: W:K.20, W:K.20 pi-Stacking: W:Y.308 ADP.21: 12 residues within 4Å: Chain X: G.15, S.16, G.17, L.18, G.158, D.159, E.216, G.303, G.304, T.305, Y.308 Ligands: MG.22 5 PLIP interactions: 5 interactions with chain X Hydrogen bonds: X:G.15, X:G.17, X:L.18, X:D.159, X:G.304

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

MG.2: 1 residues within 4Å: Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain I: Q.139 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain J: Q.139, G.158 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain K: D.13, Q.139 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.13 MG.11: 2 residues within 4Å: Chain M: G.13 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain N: G.160 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: ADP.18 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: ADP.19 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: ADP.21 No protein-ligand interaction detected (PLIP)

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: AM
Actin-related protein 2: BN
Actin-related protein 2/3 complex subunit 1B: CO
Actin-related protein 2/3 complex subunit 2: DP
Actin-related protein 2/3 complex subunit 3: EQ
Actin-related protein 2/3 complex subunit 4: FR
Actin-related protein 2/3 complex subunit 5: GS
NCK-interacting protein with SH3 domain: HT
Actin, alpha skeletal muscle: IJKLUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M
a

B
B

N
b

C
C

O
c

D
D

P
d

E
E

Q
e

F
F

R
f

G
G

S
g

H
H

T
h

I
I

J
J

K
K

L
L

U
i

V
j

W
k

X
l

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

Related Entries With Identical Sequence