SMTL ID : 8p94.1

Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-10-1-1-1-mer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 23 residues within 4Å: Chain A: I.309, R.312, L.353 Chain B: E.75, N.76, I.78, R.80, M.114, N.115, P.116, K.118, R.181, D.183 Chain J: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain J Hydrophobic interactions: B:N.76, B:I.78, B:I.78, B:P.116, J:Y.198, J:I.248 Hydrogen bonds: J:G.197, J:G.197, J:S.199, J:Q.246 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 22 residues within 4Å: Chain B: I.291, R.294, K.331 Chain J: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain K: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 10 PLIP interactions: 3 interactions with chain J, 6 interactions with chain K, 1 interactions with chain B Hydrophobic interactions: J:I.75, J:T.77, K:Y.198 Hydrogen bonds: J:D.179, K:G.197, K:G.197, K:S.199, K:S.199, K:Q.246, B:R.294 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 21 residues within 4Å: Chain H: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 Chain J: V.287, R.290 Chain K: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 11 PLIP interactions: 3 interactions with chain K, 5 interactions with chain H, 3 interactions with chain J Hydrophobic interactions: K:I.75, K:P.112, H:Y.198, H:I.248, J:V.287 Hydrogen bonds: K:D.179, H:G.197, H:G.197, H:S.199, J:R.290, J:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 16 residues within 4Å: Chain H: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain K: V.287, R.290 Chain T: G.197, Y.198, S.199, E.205, Q.246 11 PLIP interactions: 5 interactions with chain H, 4 interactions with chain T, 2 interactions with chain K Hydrophobic interactions: H:E.72, H:H.73, H:I.75, H:T.77, H:P.112 Hydrogen bonds: T:G.197, T:G.197, T:S.199, T:Q.246, K:R.290, K:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.5: 19 residues within 4Å: Chain L: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain M: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 8 PLIP interactions: 5 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:Y.198, L:I.75, L:P.112 Hydrogen bonds: M:G.197, M:G.197, M:S.199, M:S.199, L:E.72 TRP-EEP-ALA-DTH-CYS-HYP-ALA.6: 21 residues within 4Å: Chain L: V.287, R.290 Chain M: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain N: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 10 PLIP interactions: 6 interactions with chain N, 3 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: N:Y.198, N:I.248, M:I.75, M:P.112 Hydrogen bonds: N:G.197, N:G.197, N:G.197, N:S.199, M:D.179, L:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.7: 21 residues within 4Å: Chain M: V.287, R.290 Chain N: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain O: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 11 PLIP interactions: 7 interactions with chain O, 3 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: O:Y.198, O:L.242, O:I.248, N:I.75, N:I.75 Hydrogen bonds: O:G.197, O:G.197, O:G.197, O:S.199, N:D.179, M:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.8: 21 residues within 4Å: Chain N: V.287, R.290 Chain O: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 Chain P: T.194, R.196, G.197, Y.198, S.199, F.200, E.205, L.242, Q.246, I.248 9 PLIP interactions: 4 interactions with chain P, 4 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: P:Y.198, O:I.75, O:I.75, O:P.112 Hydrogen bonds: P:G.197, P:G.197, P:S.199, O:D.179, N:R.290 TRP-EEP-ALA-DTH-CYS-HYP-ALA.9: 22 residues within 4Å: Chain D: R.190 Chain O: V.287, R.290 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 15 PLIP interactions: 3 interactions with chain O, 5 interactions with chain P, 7 interactions with chain Q Hydrophobic interactions: O:V.287, P:E.72, P:I.75, P:I.75, P:P.112, Q:Y.198, Q:I.248 Hydrogen bonds: O:R.290, O:R.290, P:D.179, Q:G.197, Q:G.197, Q:G.197, Q:S.199, Q:S.199 TRP-EEP-ALA-DTH-CYS-HYP-ALA.10: 11 residues within 4Å: Chain P: V.287, R.290 Chain Q: E.72, H.73, I.75, T.77, L.110, N.111, P.112, R.177, D.179 3 PLIP interactions: 1 interactions with chain P, 2 interactions with chain Q Hydrogen bonds: P:R.290, Q:D.179 Hydrophobic interactions: Q:P.112

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

ADP.11: 25 residues within 4Å: Chain A: G.13, T.14, G.15, Y.16, K.18, G.171, D.172, G.173, G.197, R.198, T.201, K.225, K.228, E.229, G.323, G.324, S.325, M.327, F.328, R.374 Chain I: N.30, Q.37, A.41, T.43 Ligands: MG.12 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:T.14, A:T.14, A:G.15, A:Y.16, A:D.172, A:D.172, A:D.172, A:K.225, A:K.228, A:E.229, A:G.324, A:R.374, A:R.374, I:Q.37 Salt bridges: A:K.18, A:K.18, A:R.374 pi-Stacking: A:F.328 ADP.13: 20 residues within 4Å: Chain B: G.14, T.15, G.16, F.17, K.19, G.160, D.161, G.162, G.186, T.190, R.214, K.217, E.218, G.305, G.306, S.307, M.309, Y.310, K.351 Ligands: MG.14 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.14, 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, B:S.307 Salt bridges: B:K.351 pi-Stacking: B:Y.310 ADP.15: 19 residues within 4Å: Chain H: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.158, G.182, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, P.307, K.336 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.13, H:S.14, H:S.14, H:M.16, H:D.157, H:K.213, H:E.214, H:G.302, H:Y.306 Salt bridges: H:K.18, H:K.18 ADP.17: 22 residues within 4Å: Chain I: Y.84, E.91, R.94 Chain J: G.13, S.14, M.16, K.18, G.156, D.157, G.182, R.183, T.186, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.18 16 PLIP interactions: 13 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:M.16, J:M.16, J:D.157, J:D.157, J:G.182, J:T.186, J:K.213, J:G.302, J:T.303, J:K.336, I:Y.84, I:E.91, I:R.94 Salt bridges: J:K.18, J:K.18 pi-Stacking: J:Y.306 ADP.19: 19 residues within 4Å: Chain K: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.182, T.186, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.20 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:S.14, K:M.16, K:D.157, K:D.157, K:D.157, K:K.213, K:G.302, K:M.305, K:K.336 Salt bridges: K:K.18, K:K.18 pi-Stacking: K:Y.306 ADP.21: 19 residues within 4Å: Chain L: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.158, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.22 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:G.13, L:S.14, L:M.16, L:D.157, L:G.158, L:K.213, L:E.214, L:E.214, L:G.302, L:K.336 Salt bridges: L:K.18, L:K.18 pi-Stacking: L:Y.306 ADP.23: 21 residues within 4Å: Chain M: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.158, G.182, R.183, T.186, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.24 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.13, M:M.16, M:D.157, M:G.158, M:G.182, M:K.213, M:E.214, M:G.302, M:K.336 Salt bridges: M:K.18, M:K.18 pi-Stacking: M:Y.306 ADP.25: 18 residues within 4Å: Chain N: G.13, S.14, G.15, M.16, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, P.307, K.336 Ligands: MG.26 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:M.16, N:M.16, N:D.157, N:D.157, N:K.213, N:E.214, N:E.214, N:G.302, N:M.305 Salt bridges: N:K.336 ADP.27: 19 residues within 4Å: Chain O: G.13, S.14, G.15, M.16, K.18, S.155, 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.28 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:S.14, O:M.16, O:M.16, O:D.157, O:D.157, O:K.213, O:G.302, O:T.303, O:M.305, O:K.336 Salt bridges: O:K.18, O:K.18, O:K.336 pi-Stacking: O:Y.306 ADP.29: 19 residues within 4Å: Chain P: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.158, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.30 14 PLIP interactions: 14 interactions with chain P Hydrogen bonds: P:G.13, P:S.14, P:G.15, P:M.16, P:D.157, P:G.158, P:K.213, P:G.302, P:M.305, P:K.336, P:K.336 Salt bridges: P:K.18, P:K.18 pi-Stacking: P:Y.306 ADP.32: 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.31 12 PLIP interactions: 12 interactions with chain Q Hydrogen bonds: Q:G.13, Q:S.14, Q:G.15, Q:M.16, Q:D.157, Q:D.157, Q:D.157, Q:K.213, Q:G.302, Q:K.336 Salt bridges: Q:K.18, Q:K.18 ADP.33: 20 residues within 4Å: Chain T: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, C.217, G.301, G.302, T.303, M.305, Y.306, P.307, K.336 Ligands: MG.34 13 PLIP interactions: 13 interactions with chain T Hydrogen bonds: T:S.14, T:S.14, T:S.14, T:M.16, T:D.157, T:D.157, T:R.210, T:R.210, T:G.302, T:M.305, T:K.336 Salt bridges: T:K.18, T:K.18

12 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain A: G.13, Q.144, G.171 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: D.12, Q.141 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain H: G.13, Q.137, G.156 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain J: Q.137, D.154, G.156, G.301, V.339 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain K: G.13, Q.137, G.156 Ligands: ADP.19 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain L: G.13, Q.137, G.156 Ligands: ADP.21 No protein-ligand interaction detected (PLIP) MG.24: 6 residues within 4Å: Chain M: G.13, Q.137, D.154, G.156, V.339 Ligands: ADP.23 No protein-ligand interaction detected (PLIP) MG.26: 6 residues within 4Å: Chain N: Q.137, D.154, G.156, G.301, V.339 Ligands: ADP.25 No protein-ligand interaction detected (PLIP) MG.28: 6 residues within 4Å: Chain O: Q.137, D.154, G.156, G.301, V.339 Ligands: ADP.27 No protein-ligand interaction detected (PLIP) MG.30: 6 residues within 4Å: Chain P: D.11, G.13, K.18, Q.137, V.339 Ligands: ADP.29 No protein-ligand interaction detected (PLIP) MG.31: 7 residues within 4Å: Chain Q: G.13, K.18, G.156, D.157, G.301, G.302 Ligands: ADP.32 No protein-ligand interaction detected (PLIP) MG.34: 5 residues within 4Å: Chain T: K.18, Q.137, G.156, V.339 Ligands: ADP.33 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, T. et al., Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-01-03

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-like protein: G
Actin, cytoplasmic 1: HJKLMNOPQT
Src substrate cortactin: I
F-actin-capping protein subunit alpha-1: R
Isoform 2 of F-actin-capping protein subunit beta: S

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

J
J

K
K

L
N

M
O

N
P

O
Q

P
R

Q
S

T
W

I
I

R
U

S
V

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-like protein

Actin, cytoplasmic 1

Src substrate cortactin

F-actin-capping protein subunit alpha-1

Isoform 2 of F-actin-capping protein subunit beta

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