SMTL ID : 8rty.1

Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-1-mer

Ligands

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

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 13 residues within 4Å: Chain A: E.71, H.72, I.74, R.176 Chain B: T.193, R.195, G.196, Y.197, S.198, E.204, L.241, Q.245, I.247 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.197, B:Y.197, B:L.241, B:I.247 Hydrogen bonds: B:G.196, B:G.196, B:S.198, A:D.178 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 16 residues within 4Å: Chain A: R.289 Chain B: E.71, H.72, I.74, L.109, P.111, R.176 Chain C: T.193, R.195, G.196, Y.197, S.198, F.199, E.204, L.241, Q.245 14 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: B:I.74, B:P.111, C:Y.197, C:Y.197, C:F.199, C:F.199, C:L.241 Hydrogen bonds: A:R.289, A:R.289, C:G.196, C:G.196, C:G.196, C:S.198, C:Q.245 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 13 residues within 4Å: Chain B: V.286, R.289 Chain C: E.71, H.72, I.74, L.109, P.111, R.176 Chain D: T.193, R.195, G.196, Y.197, S.198 11 PLIP interactions: 5 interactions with chain D, 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: D:Y.197, B:V.286, C:E.71, C:I.74, C:P.111 Hydrogen bonds: D:G.196, D:G.196, D:G.196, D:S.198, B:R.289, B:R.289

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

ADP.4: 18 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.5, PO4.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.12, A:G.14, A:M.15, A:D.156, A:D.156, A:R.209, A:K.212, A:E.213, A:G.301 Salt bridges: A:K.17, A:K.17, A:K.335 ADP.7: 18 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.8, PO4.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.13, B:G.14, B:M.15, B:D.156, B:D.156, B:K.212, B:E.213, B:G.301 Salt bridges: B:K.17, B:K.17, B:K.335 ADP.10: 16 residues within 4Å: Chain C: G.12, S.13, G.14, M.15, K.17, G.155, D.156, K.212, E.213, G.301, T.302, M.304, Y.305, K.335 Ligands: MG.11, PO4.12 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.14, C:M.15, C:D.156, C:D.156, C:E.213, C:G.301, C:K.335 Salt bridges: C:K.17, C:K.17 ADP.13: 14 residues within 4Å: Chain D: G.12, S.13, M.15, K.17, D.156, R.209, K.212, E.213, G.300, G.301, T.302, M.304, K.335 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.13, D:M.15, D:M.15, D:D.156, D:D.156, D:K.212, D:E.213, D:G.301, D:K.335 Salt bridges: D:K.17, D:K.17

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

MG.5: 3 residues within 4Å: Chain A: G.155 Ligands: ADP.4, PO4.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: G.155, D.156 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.136, D.153 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.12, S.13, Q.136, D.153, G.155, D.156, G.157, V.158 Ligands: ADP.4, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.13, A:Q.136, A:Q.136, A:D.156, A:G.157, A:V.158 PO4.9: 8 residues within 4Å: Chain B: S.13, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.7, MG.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.13, B:Q.136, B:Q.136, B:G.155, B:D.156, B:G.157, B:V.158 PO4.12: 9 residues within 4Å: Chain C: G.12, S.13, Q.136, G.155, D.156, G.157, V.158 Ligands: ADP.10, MG.11 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.13, C:S.13, C:Q.136, C:D.156, C:G.157, C:V.158, C:V.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Molecular mechanism of actin filament elongation by formins. Science (2024)

Release Date

2024-04-10

Peptides

Actin, cytoplasmic 1, N-terminally processed: ABCD
Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12: EF
Profilin-1: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
P

Actin, cytoplasmic 1, N-terminally processed

Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12

Profilin-1

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