SMTL ID : 7utj.1

Cryogenic electron microscopy 3D map of F-actin bound by human dimeric alpha-catenin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: 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.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:D.159, A:D.159, A:D.159, A:K.215, A:E.216, A:G.304, A:T.305, A:M.307, A:K.338 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.3: 18 residues within 4Å: Chain B: 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.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:D.159, B:D.159, B:D.159, B:K.215, B:E.216, B:G.304, B:T.305, B:M.307, B:K.338 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.5: 18 residues within 4Å: Chain C: 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.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:D.159, C:D.159, C:D.159, C:K.215, C:E.216, C:G.304, C:T.305, C:M.307, C:K.338 Water bridges: C:T.188 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308 ADP.7: 18 residues within 4Å: Chain D: 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.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.16, D:G.17, D:L.18, D:D.159, D:D.159, D:D.159, D:K.215, D:E.216, D:G.304, D:T.305, D:M.307, D:K.338 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.9: 18 residues within 4Å: Chain E: 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.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.16, E:G.17, E:L.18, E:D.159, E:D.159, E:D.159, E:K.215, E:E.216, E:G.304, E:T.305, E:M.307, E:K.338 Salt bridges: E:K.20, E:K.20 pi-Stacking: E:Y.308 ADP.11: 19 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, S.157, 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.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.16, F:G.17, F:L.18, F:D.159, F:D.159, F:K.215, F:E.216, F:G.304, F:T.305, F:M.307, F:K.338 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.139, D.156 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.139 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: D.13, Q.139 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: D.13, Q.139 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: Q.139 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: Q.139, D.156 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rangarajan, E.S. et al., Distinct inter-domain interactions of dimeric versus monomeric alpha-catenin link cell junctions to filaments. Commun Biol (2023)

Release Date

2023-03-08

Peptides

Actin, alpha skeletal muscle: ABCDEF
Catenin alpha-1: GHIJKL

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
K

K
L

L
Z

Actin, alpha skeletal muscle

Catenin alpha-1

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