SMTL ID : 8ru2.1

Structure of the F-actin barbed end bound by formin mDia1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: G.12, S.13, G.14, M.15, K.17, G.155, D.156, G.181, K.212, E.213, G.300, G.301, T.302, Y.305, K.335 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.13, A:G.14, A:M.15, A:D.156, A:D.156, A:K.212, A:K.212, A:E.213, A:G.301 Salt bridges: A:K.17, A:K.17, A:K.335 ADP.3: 15 residues within 4Å: Chain B: G.12, S.13, G.14, M.15, K.17, G.155, D.156, K.212, E.213, G.300, G.301, T.302, M.304, Y.305 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.13, B:G.14, B:D.156, B:D.156, B:D.156, B:K.212, B:G.301, B:T.302, B:M.304 Salt bridges: B:K.17, B:K.17 pi-Stacking: B:Y.305 ADP.5: 16 residues within 4Å: Chain C: G.12, S.13, 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.13, C:M.15, C:D.156, C:D.156, C:K.212, C:E.213, C:G.301, C:M.304, C:K.335 Salt bridges: C:K.17, C:K.17 pi-Stacking: C:Y.305

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.10, K.17 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: D.10, K.17 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.136, V.338 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

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: ABC
Methylated-DNA--protein-cysteine methyltransferase,Protein diaphanous homolog 1: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

Actin, cytoplasmic 1, N-terminally processed

Methylated-DNA--protein-cysteine methyltransferase,Protein diaphanous homolog 1

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