SMTL ID : 9qfb.1

Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.12, S.13, G.14, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.13, A:G.14, A:M.15, A:D.156, A:D.156, A:D.156, A:K.212, A:E.213, A:G.301, A:T.302, A:K.335 Salt bridges: A:K.17, A:K.17 pi-Stacking: A:Y.305 ADP.3: 17 residues within 4Å: Chain B: G.12, S.13, G.14, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.13, B:G.14, B:M.15, B:D.156, B:D.156, B:D.156, B:K.212, B:E.213, B:G.301, B:T.302, B:K.335 Salt bridges: B:K.17, B:K.17 pi-Stacking: B:Y.305 ADP.5: 17 residues within 4Å: Chain C: G.12, S.13, G.14, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.13, C:G.14, C:M.15, C:D.156, C:D.156, C:K.212, C:E.213, C:G.301, C:T.302, C:K.335 Salt bridges: C:K.17, C:K.17 pi-Stacking: C:Y.305 ADP.7: 18 residues within 4Å: Chain D: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.12, D:G.14, D:M.15, D:D.156, D:D.156, D:K.212, D:E.213, D:G.301, D:T.302, D:K.335 Salt bridges: D:K.17, D:K.17 pi-Stacking: D:Y.305 ADP.9: 17 residues within 4Å: Chain E: G.12, S.13, G.14, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.13, E:G.14, E:M.15, E:D.156, E:D.156, E:K.212, E:E.213, E:G.301, E:K.335 Salt bridges: E:K.17, E:K.17 pi-Stacking: E:Y.305 ADP.11: 18 residues within 4Å: Chain F: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.12, F:G.14, F:M.15, F:D.156, F:D.156, F:K.212, F:E.213, F:G.301, F:K.335 Salt bridges: F:K.17, F:K.17 pi-Stacking: F:Y.305 ADP.13: 17 residues within 4Å: Chain G: G.12, S.13, G.14, M.15, K.17, G.155, D.156, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.14, G:M.15, G:D.156, G:D.156, G:K.212, G:E.213, G:G.301, G:K.335 Salt bridges: G:K.17, G:K.17 pi-Stacking: G:Y.305

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.17, Q.136 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.136 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: K.17, Q.136 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: K.17, Q.136 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: Q.136 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: K.17, Q.136 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: K.17, Q.136 Ligands: ADP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Choreography of rapid actin filament disassembly by coronin, cofilin and AIP1. To Be Published

Release Date

2025-10-08

Peptides

Actin, cytoplasmic 1, N-terminally processed: ABCDEFG
Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase: HIJKLMN

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

Actin, cytoplasmic 1, N-terminally processed

Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase

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