› 5nbm

X-ray diffraction
3.4Å resolution

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

Released:
DOI: 10.2210/pdb5nbm/pdb
PDB entry 5nbm coloured by chain, front view.
PDB entry 5nbm coloured by chain, side view.
PDB entry 5nbm coloured by chain, top view.
Source organisms:
Primary publication:
The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.
Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP
Nat Struct Mol Biol 25 823-832 (2018)
PMID: 30177756

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-211403 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Actin-related protein 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 489 amino acids
Theoretical weight: 54.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P80428 (Residues: 1-489; Coverage: 100%)
Gene names: ACT3, ARP4, J1012, YJL081C
Sequence domains: Actin
Structure domains:
Actin Chains: C, D
Molecule details ›
Chains: C, D
Length: 375 amino acids
Theoretical weight: 41.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P60010 (Residues: 1-375; Coverage: 100%)
Gene names: ABY1, ACT1, END7, YFL039C
Sequence domains: Actin
Structure domains:
nAct-Nanobody Chains: E, F
Molecule details ›
Chains: E, F
Length: 159 amino acids
Theoretical weight: 17.16 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli
Unknown peptide Chains: G, H
Molecule details ›
Chains: G, H
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Trichoplusia ni
Expression system: Trichoplusia ni

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand ATP 4 x ATP
1 modified residue:
Ligand HIC 2 x HIC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P65
Unit cell:
a: 190.581Å b: 190.581Å c: 220.616Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.154 0.152 0.193
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

12 review citations

Emerging Properties and Functions of Actin and Actin Filaments Inside the Nucleus.
Ulferts et al. (2021)
11 more

1 mention without citation

How gene duplication diversifies the landscape of protein oligomeric state and function.
Mallik et al. (2022)