SMTL ID : 9i2b.1

SPIN90-Arp2/3 nucleated bidirectional actin filaments

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-4-2-2-2-mer

Ligands

4 x TRP- EEP- ALA- DTH- CYS- HYP- ALA: Phalloidin(Non-covalent)

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 22 residues within 4Å: Chain A: E.75, N.76, I.78, R.80, M.114, N.115, P.116, R.181, D.183 Chain F: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 Chain J: I.309, R.312, L.353 8 PLIP interactions: 6 interactions with chain F, 1 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: F:Y.198, F:Y.198, F:I.248, A:I.78, J:I.309 Hydrogen bonds: F:G.197, F:G.197, F:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 22 residues within 4Å: Chain A: I.291, R.294, K.331 Chain F: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain G: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 12 PLIP interactions: 5 interactions with chain F, 4 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: F:I.75, F:I.75, F:T.77, F:P.112, G:Y.198, A:I.291 Hydrogen bonds: F:D.179, G:G.197, G:G.197, G:S.199, A:R.294, A:R.294 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 22 residues within 4Å: Chain K: E.75, N.76, I.78, R.80, M.114, N.115, P.116, R.181, D.183 Chain P: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 Chain T: I.309, R.312, L.353 8 PLIP interactions: 1 interactions with chain T, 1 interactions with chain K, 6 interactions with chain P Hydrophobic interactions: T:I.309, K:I.78, P:Y.198, P:Y.198, P:I.248 Hydrogen bonds: P:G.197, P:G.197, P:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 22 residues within 4Å: Chain K: I.291, R.294, K.331 Chain P: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain Q: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 12 PLIP interactions: 4 interactions with chain Q, 3 interactions with chain K, 5 interactions with chain P Hydrophobic interactions: Q:Y.198, K:I.291, P:I.75, P:I.75, P:T.77, P:P.112 Hydrogen bonds: Q:G.197, Q:G.197, Q:S.199, K:R.294, K:R.294, P:D.179

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

ADP.5: 21 residues within 4Å: Chain A: G.14, T.15, G.16, F.17, K.19, G.160, D.161, G.162, G.186, R.214, K.217, E.218, G.305, G.306, S.307, M.309, Y.310, K.351 Chain D: R.32 Chain I: N.52 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.15, A:G.16, A:F.17, A:D.161, A:D.161, A:K.217, A:G.306, A:K.351 Salt bridges: A:K.19, A:K.19 pi-Stacking: A:Y.310 ADP.7: 19 residues within 4Å: Chain F: D.11, G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.15, F:M.16, F:D.157, F:D.157, F:K.213, F:G.302, F:K.336 Salt bridges: F:K.18, F:K.18 pi-Stacking: F:Y.306 ADP.9: 19 residues within 4Å: Chain G: D.11, G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.15, G:M.16, G:D.157, G:K.213, G:G.302, G:K.336 Salt bridges: G:K.18, G:K.18 pi-Stacking: G:Y.306 ADP.11: 18 residues within 4Å: Chain J: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, G.197, K.225, K.228, E.229, G.323, G.324, S.325, M.327, F.328, R.374 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:G.15, J:Y.16, J:D.172, J:K.228, J:E.229, J:G.324 Salt bridges: J:K.18, J:K.18, J:R.374 pi-Stacking: J:F.328 ADP.13: 21 residues within 4Å: Chain K: G.14, T.15, G.16, F.17, K.19, G.160, D.161, G.162, G.186, R.214, K.217, E.218, G.305, G.306, S.307, M.309, Y.310, K.351 Chain N: R.32 Chain S: N.52 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:T.15, K:G.16, K:F.17, K:D.161, K:D.161, K:K.217, K:G.306, K:K.351 Salt bridges: K:K.19, K:K.19 pi-Stacking: K:Y.310 ADP.15: 19 residues within 4Å: Chain P: D.11, G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.16 10 PLIP interactions: 10 interactions with chain P Hydrogen bonds: P:G.15, P:M.16, P:D.157, P:D.157, P:K.213, P:G.302, P:K.336 Salt bridges: P:K.18, P:K.18 pi-Stacking: P:Y.306 ADP.17: 19 residues within 4Å: Chain Q: D.11, G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain Q Hydrogen bonds: Q:G.15, Q:M.16, Q:D.157, Q:K.213, Q:G.302, Q:K.336 Salt bridges: Q:K.18, Q:K.18 pi-Stacking: Q:Y.306 ADP.19: 18 residues within 4Å: Chain T: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, G.197, K.225, K.228, E.229, G.323, G.324, S.325, M.327, F.328, R.374 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain T Hydrogen bonds: T:G.15, T:Y.16, T:D.172, T:K.228, T:E.229, T:G.324 Salt bridges: T:K.18, T:K.18, T:R.374 pi-Stacking: T:F.328

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

MG.6: 3 residues within 4Å: Chain A: K.19, Q.141 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain F: D.11, K.18, Q.137, D.154, G.156 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain G: D.11, K.18, Q.137, D.154, G.156 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain J: D.11, K.18, Q.144 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain K: K.19, Q.141 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 6 residues within 4Å: Chain P: D.11, K.18, Q.137, D.154, G.156 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain Q: D.11, K.18, Q.137, D.154, G.156 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain T: D.11, K.18, Q.144 Ligands: ADP.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, T. et al., Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers in metazoans. To Be Published

Release Date

2025-09-03

Peptides

Actin-related protein 2: AK
Actin-related protein 2/3 complex subunit 2: BL
Actin-related protein 2/3 complex subunit 3: CM
Actin-related protein 2/3 complex subunit 4: DN
Actin-related protein 2/3 complex subunit 5-like protein: EO
Actin, cytoplasmic 1: FGPQ
NCK-interacting protein with SH3 domain: HR
Actin-related protein 2/3 complex subunit 1B: IS
Actin-related protein 3: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

K
L

B
D

L
N

C
E

M
O

D
F

N
P

E
G

O
Q

F
I

G
J

P
S

Q
T

H
H

R
R

I
C

S
M

J
A

T
K

Actin-related protein 2

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-like protein

Actin, cytoplasmic 1

NCK-interacting protein with SH3 domain

Actin-related protein 2/3 complex subunit 1B

Actin-related protein 3

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