› 7v9f

X-ray diffraction
2.5Å resolution

Selenomethionine mutant (L740Sem) of BEN4 domain of protein Bend3 with DNA

Released:
DOI: 10.2210/pdb7v9f/pdb
Model geometry
Fit model/data
PDB entry 7v9f coloured by chain, front view.
PDB entry 7v9f coloured by chain, side view.
PDB entry 7v9f coloured by chain, top view.
Source organisms:
Primary publication:
Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.
Zhang J, Zhang Y, You Q, Huang C, Zhang T, Wang M, Zhang T, Yang X, Xiong J, Li Y, Liu CP, Zhang Z, Xu RM, Zhu B
Science 375 1053-1058 (2022)
PMID: 35143257

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-279186 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
BEN domain-containing protein 3 Chain: A
Molecule details ›
Chain: A
Length: 114 amino acids
Theoretical weight: 13.65 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6PAL0 (Residues: 712-825; Coverage: 14%)
Gene names: Bend3, Kiaa1553
Sequence domains: BEN domain
DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3') Chain: C

Ligands and Environments

1 bound ligand:
Ligand CIT 2 x CIT
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P6222
Unit cell:
a: 96.831Å b: 96.831Å c: 141.693Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.178 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

Epigenetic regulation of aging: implications for interventions of aging and diseases.
Wang et al. (2022)
9 more

1 mention without citation

Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA.
Baek et al. (2024)