SMTL ID : 7tpt.1

Single-particle Cryo-EM structure of Arp2/3 complex at branched-actin junction.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-14-mer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 10 residues within 4Å: Chain A: I.309 Chain B: E.75, N.76, I.78, R.80, P.116, R.181 Chain H: G.199, Y.200, S.201 11 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, 5 interactions with chain H Hydrophobic interactions: B:E.75, B:I.78, B:I.78, B:P.116, A:I.309, H:Y.200 Hydrogen bonds: B:R.80, H:G.199, H:G.199, H:G.199, H:S.201 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 12 residues within 4Å: Chain B: I.291, R.294 Chain H: E.74, I.77, L.112, R.179, D.181 Chain I: T.196, G.199, Y.200, S.201, Q.248 11 PLIP interactions: 3 interactions with chain B, 5 interactions with chain I, 3 interactions with chain H Hydrophobic interactions: B:I.291, I:T.196, I:Y.200, H:E.74, H:I.77 Hydrogen bonds: B:R.294, B:R.294, I:G.199, I:G.199, I:S.201, H:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 9 residues within 4Å: Chain H: I.289, R.292 Chain I: E.74, I.77, L.112, R.179 Chain J: G.199, Y.200, S.201 9 PLIP interactions: 5 interactions with chain J, 2 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: J:S.201, H:I.289 Hydrogen bonds: J:G.199, J:G.199, J:G.199, J:S.201, H:R.292, I:E.74, I:R.179 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 6 residues within 4Å: Chain I: M.285, R.292 Chain J: E.74 Chain K: G.199, Y.200, S.201 7 PLIP interactions: 1 interactions with chain I, 5 interactions with chain K, 1 interactions with chain J Hydrogen bonds: I:R.292, K:G.199, K:G.199, K:G.199, K:S.201 Hydrophobic interactions: K:Y.200, J:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.5: 1 residues within 4Å: Chain K: E.74 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.6: 10 residues within 4Å: Chain L: E.74, I.77, I.78, L.112, N.113, P.114 Chain M: T.196, G.199, Y.200, S.201 5 PLIP interactions: 3 interactions with chain M, 2 interactions with chain L Hydrogen bonds: M:G.199, M:G.199, M:S.201 Hydrophobic interactions: L:I.77, L:P.114 TRP-EEP-ALA-DTH-CYS-HYP-ALA.7: 6 residues within 4Å: Chain M: E.74 Chain N: G.199, S.201, F.202, E.207, Q.248 5 PLIP interactions: 1 interactions with chain M, 4 interactions with chain N Hydrophobic interactions: M:E.74, N:F.202 Hydrogen bonds: N:G.199, N:S.201, N:Q.248 TRP-EEP-ALA-DTH-CYS-HYP-ALA.8: 8 residues within 4Å: Chain N: E.74, I.77, P.114 Chain O: T.196, G.199, Y.200, S.201, Q.248 9 PLIP interactions: 7 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: O:T.196, O:Y.200, O:Y.200, N:I.77, N:P.114 Hydrogen bonds: O:G.199, O:G.199, O:S.201, O:Q.248 TRP-EEP-ALA-DTH-CYS-HYP-ALA.9: 9 residues within 4Å: Chain N: R.292 Chain O: E.74, I.77, R.179 Chain P: G.199, Y.200, S.201, E.207, Q.248 7 PLIP interactions: 4 interactions with chain P, 2 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: P:Y.200, O:I.77 Hydrogen bonds: P:G.199, P:G.199, P:S.201, O:E.74, N:R.292 TRP-EEP-ALA-DTH-CYS-HYP-ALA.10: 11 residues within 4Å: Chain P: E.74, H.75, I.77, P.114, R.179, D.181 Chain Q: G.199, Y.200, S.201, E.207, Q.248 6 PLIP interactions: 4 interactions with chain Q, 2 interactions with chain P Hydrophobic interactions: Q:Y.200, P:I.77, P:P.114 Hydrogen bonds: Q:G.199, Q:S.201, Q:Q.248 TRP-EEP-ALA-DTH-CYS-HYP-ALA.11: 9 residues within 4Å: Chain Q: E.74, I.77, R.179, D.181 Chain R: G.199, Y.200, S.201, Q.248, I.250 8 PLIP interactions: 5 interactions with chain R, 1 interactions with chain P, 2 interactions with chain Q Hydrophobic interactions: R:Y.200, R:I.250, Q:I.77 Hydrogen bonds: R:G.199, R:G.199, R:S.201, P:R.292, Q:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.12: 8 residues within 4Å: Chain Q: R.292 Chain R: E.74, I.77, R.179 Chain S: G.199, Y.200, S.201, Q.248 10 PLIP interactions: 3 interactions with chain R, 6 interactions with chain S, 1 interactions with chain Q Hydrophobic interactions: R:E.74, R:I.77, S:Y.200, S:Y.200 Hydrogen bonds: R:E.74, S:G.199, S:G.199, S:S.201, S:Q.248, Q:R.292 TRP-EEP-ALA-DTH-CYS-HYP-ALA.13: 8 residues within 4Å: Chain S: E.74, I.77, T.79, R.179, D.181 Chain T: G.199, Y.200, S.201 10 PLIP interactions: 4 interactions with chain S, 6 interactions with chain T Hydrophobic interactions: S:E.74, S:I.77, T:Y.200, T:S.201 Hydrogen bonds: S:E.74, S:E.74, T:G.199, T:G.199, T:G.199, T:S.201 TRP-EEP-ALA-DTH-CYS-HYP-ALA.14: 3 residues within 4Å: Chain S: R.292 Chain T: E.74 Chain U: G.199 3 PLIP interactions: 1 interactions with chain T, 2 interactions with chain U Hydrophobic interactions: T:E.74 Hydrogen bonds: U:G.199, U:S.201 TRP-EEP-ALA-DTH-CYS-HYP-ALA.15: 1 residues within 4Å: Chain U: E.74 1 PLIP interactions: 1 interactions with chain U Hydrophobic interactions: U:E.74

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

MG.16: 3 residues within 4Å: Chain A: S.170, G.171 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain B: D.12 Ligands: ADP.19 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain H: Q.139, D.156 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain I: G.15 Ligands: ADP.23 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain J: G.15 Ligands: ADP.25 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain K: G.15 Ligands: ADP.27 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain L: G.15 Ligands: ADP.29 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Ligands: ADP.31 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain N: D.13, G.15, Q.139 Ligands: ADP.33 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain O: G.15, S.16, Q.139 Ligands: ADP.35 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain P: G.15, S.16, Q.139 Ligands: ADP.37 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain Q: G.15, Q.139 Ligands: ADP.39 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain R: Q.139 Ligands: ADP.41 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain S: G.15, S.16, Q.139 Ligands: ADP.43 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Ligands: ADP.45 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain U: G.15 Ligands: ADP.47 No protein-ligand interaction detected (PLIP)

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

ADP.17: 17 residues within 4Å: Chain A: G.13, T.14, G.15, Y.16, K.18, S.170, G.171, D.172, G.197, V.227, K.228, G.324, S.325, M.327, F.328, R.374 Ligands: MG.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.15, A:D.172, A:D.172, A:K.228 Salt bridges: A:K.18, A:R.374 ADP.19: 12 residues within 4Å: Chain B: G.14, T.15, F.17, G.160, D.161, R.214, K.217, E.218, G.306, S.307, Y.310 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.14, B:T.15, B:D.161, B:D.161, B:R.214, B:R.214, B:G.306 pi-Stacking: B:Y.310 pi-Cation interactions: B:R.214 ADP.20: 15 residues within 4Å: Chain H: G.15, S.16, K.20, Q.139, S.157, G.158, D.159, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: MG.21 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.16, H:Q.139, H:S.157, H:D.159, H:D.159, H:K.215, H:E.216, H:E.216, H:G.304, H:T.305, H:T.305, H:K.338 Salt bridges: H:K.20, H:K.20 ADP.23: 14 residues within 4Å: Chain I: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, T.305, Y.308, K.338 Ligands: MG.22 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:S.16, I:G.17, I:D.159, I:D.159, I:K.215, I:E.216, I:G.304 Salt bridges: I:K.20, I:K.20 ADP.25: 12 residues within 4Å: Chain J: G.15, S.16, G.17, L.18, G.158, D.159, G.160, E.216, G.303, G.304, T.305 Ligands: MG.24 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:S.16, J:G.17, J:D.159, J:G.160, J:E.216, J:G.304 ADP.27: 9 residues within 4Å: Chain K: G.15, S.16, G.17, L.18, G.158, D.159, E.216, G.304 Ligands: MG.26 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:S.16, K:G.17, K:D.159, K:G.304 ADP.29: 10 residues within 4Å: Chain L: G.15, S.16, G.17, L.18, G.158, D.159, E.216, G.304, T.305 Ligands: MG.28 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:S.16, L:G.17, L:D.159, L:E.216, L:G.304 ADP.31: 10 residues within 4Å: Chain M: G.15, S.16, G.17, L.18, G.158, D.159, E.216, G.304, T.305 Ligands: MG.30 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:S.16, M:D.159, M:E.216, M:G.304 ADP.33: 15 residues within 4Å: Chain N: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, K.338 Ligands: MG.32 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:S.16, N:G.17, N:D.159, N:D.159, N:K.215, N:G.304, N:K.338, N:K.338 Salt bridges: N:K.20, N:K.20 ADP.35: 15 residues within 4Å: Chain O: D.13, G.15, S.16, G.17, K.20, G.158, D.159, K.215, E.216, G.303, G.304, T.305, Y.308, K.338 Ligands: MG.34 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:S.16, O:G.17, O:D.159, O:D.159, O:D.159, O:D.159, O:K.215, O:E.216, O:G.304, O:K.338 Salt bridges: O:K.20, O:K.20 ADP.37: 17 residues within 4Å: Chain P: G.15, S.16, G.17, 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.36 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:S.16, P:G.17, P:D.159, P:D.159, P:D.159, P:R.212, P:K.215, P:G.304, P:K.338 Salt bridges: P:K.20, P:K.20 ADP.39: 14 residues within 4Å: Chain Q: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.304, T.305, K.338 Ligands: MG.38 12 PLIP interactions: 12 interactions with chain Q Hydrogen bonds: Q:S.16, Q:G.17, Q:L.18, Q:D.159, Q:D.159, Q:R.212, Q:K.215, Q:G.304, Q:K.338, Q:K.338 Salt bridges: Q:K.20, Q:K.20 ADP.41: 16 residues within 4Å: Chain R: G.15, S.16, G.17, L.18, K.20, G.158, D.159, R.212, K.215, E.216, G.303, G.304, T.305, M.307, K.338 Ligands: MG.40 10 PLIP interactions: 10 interactions with chain R Hydrogen bonds: R:S.16, R:G.17, R:D.159, R:D.159, R:K.215, R:G.304, R:K.338, R:K.338 Salt bridges: R:K.20, R:K.20 ADP.43: 13 residues within 4Å: Chain S: G.15, S.16, G.17, L.18, K.20, G.158, D.159, E.216, G.304, T.305, Y.308, K.338 Ligands: MG.42 9 PLIP interactions: 9 interactions with chain S Hydrogen bonds: S:S.16, S:G.17, S:D.159, S:D.159, S:G.304, S:K.338, S:K.338 Salt bridges: S:K.20, S:K.20 ADP.45: 12 residues within 4Å: Chain T: G.15, S.16, G.17, L.18, G.158, D.159, G.184, E.216, G.303, G.304, T.305 Ligands: MG.44 5 PLIP interactions: 5 interactions with chain T Hydrogen bonds: T:S.16, T:G.17, T:D.159, T:E.216, T:G.304 ADP.47: 11 residues within 4Å: Chain U: G.15, S.16, G.17, L.18, G.158, D.159, E.216, G.303, G.304, T.305 Ligands: MG.46 5 PLIP interactions: 5 interactions with chain U Hydrogen bonds: U:S.16, U:G.17, U:D.159, U:E.216, U:G.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, B. et al., Structure of Arp2/3 complex at a branched actin filament junction resolved by single-particle cryo-electron microscopy. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-05-25

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
Actin, alpha skeletal muscle: HIJKLMNOPQRSTU

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

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

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

Actin, alpha skeletal muscle

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