SMTL ID : 5nbm.1 (1 other biounit)

Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.159 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain B: Q.137 Ligands: ATP.4 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: G.22, S.23, Y.24, T.25, G.78, G.161, H.162, D.163, T.164, G.187, Q.240, K.243, E.244, G.412, G.413, T.414, S.416, I.417, Q.449 Ligands: CA.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.23, A:Y.24, A:T.25, A:G.78, A:H.162, A:D.163, A:T.164, A:Q.240, A:K.243, A:G.413, A:T.414, A:S.416 ATP.4: 19 residues within 4Å: Chain B: G.13, S.14, G.15, M.16, K.18, G.156, D.157, G.158, V.159, R.210, K.213, E.214, G.301, G.302, T.303, M.305, F.306, K.336 Ligands: CA.3 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:M.16, B:G.156, B:D.157, B:D.157, B:G.158, B:V.159, B:R.210, B:K.213, B:E.214, B:E.214, B:G.302, B:T.303, B:K.336 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knoll, K.R. et al., The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-08-22

Peptides

Actin-related protein 4: A
Actin: B
nAct-Nanobody: C
Unknown peptide: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
F

D
G

Actin-related protein 4

Actin

nAct-Nanobody

Unknown peptide

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