SMTL ID : 8rtt.1

Structure of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 16 residues within 4Å: Chain A: E.72, H.73, I.75, T.77, L.110, P.112, R.177 Chain B: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246, I.248 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.198, B:L.242, B:I.248, A:I.75, A:I.75, A:P.112 Hydrogen bonds: B:G.197, B:G.197, B:G.197, B:S.199, B:Q.246 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 16 residues within 4Å: Chain A: R.290 Chain B: E.72, I.75, T.77, L.110, P.112, R.177 Chain C: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246, I.248 13 PLIP interactions: 2 interactions with chain A, 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:R.290, A:R.290, C:G.197, C:G.197, C:G.197, C:S.199, C:Q.246 Hydrophobic interactions: C:Y.198, C:Y.198, C:L.242, C:I.248, B:I.75, B:P.112 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 15 residues within 4Å: Chain B: V.287, R.290 Chain C: E.72, I.75, L.110, P.112, R.177 Chain D: T.194, R.196, G.197, Y.198, S.199, E.205, L.242, Q.246 13 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: C:I.75, C:P.112, B:V.287, D:Y.198, D:Y.198, D:L.242 Hydrogen bonds: B:R.290, B:R.290, D:G.197, D:G.197, D:G.197, D:S.199, D:Q.246

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

ADP.4: 17 residues within 4Å: Chain A: G.13, S.14, G.15, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, Y.306, K.336 Ligands: MG.5, PO4.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:M.16, A:D.157, A:D.157, A:K.213, A:E.214, A:G.302 Salt bridges: A:K.18, A:K.18, A:K.336 ADP.7: 18 residues within 4Å: Chain B: G.13, S.14, G.15, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.8, PO4.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:M.16, B:D.157, B:D.157, B:K.213, B:G.302 Salt bridges: B:K.18, B:K.18, B:K.336 ADP.10: 17 residues within 4Å: Chain C: G.13, S.14, G.15, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, Y.306, K.336 Ligands: MG.11, PO4.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.15, C:M.16, C:D.157, C:D.157, C:K.213, C:E.214, C:G.302, C:K.336 Salt bridges: C:K.18, C:K.18 ADP.13: 16 residues within 4Å: Chain D: G.13, S.14, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.14, D:M.16, D:D.157, D:D.157, D:K.213, D:E.214, D:G.302, D:K.336 Salt bridges: D:K.18, D:K.18, D:K.336

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

MG.5: 2 residues within 4Å: Ligands: ADP.4, PO4.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: Q.137, D.154 Ligands: ADP.7, PO4.9 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Ligands: ADP.10, PO4.12 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain D: Q.137, D.154 Ligands: ADP.13 No protein-ligand interaction detected (PLIP)

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 10 residues within 4Å: Chain A: G.13, S.14, Q.137, D.154, G.156, D.157, G.158, V.159 Ligands: ADP.4, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.14, A:Q.137, A:D.157, A:G.158, A:V.159, A:V.159 PO4.9: 7 residues within 4Å: Chain B: S.14, Q.137, D.157, G.158, V.159 Ligands: ADP.7, MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.14, B:Q.137, B:Q.137, B:D.157, B:G.158, B:V.159 PO4.12: 10 residues within 4Å: Chain C: G.13, S.14, Q.137, D.154, G.156, D.157, G.158, V.159 Ligands: ADP.10, MG.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.14, C:S.14, C:Q.137, C:D.157, C:G.158, C:V.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Mechanism of formin-mediated processive elongation of actin filaments revealed by cryo-EM. To Be Published

Release Date

2024-04-10

Peptides

Actin, cytoplasmic 1, N-terminally processed: ABCD
Cell division control protein 12: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Actin, cytoplasmic 1, N-terminally processed

Cell division control protein 12