› 6fas

X-ray diffraction
1.9Å resolution

Crystal structure of VAL1 B3 domain in complex with cognate DNA

Released:
DOI: 10.2210/pdb6fas/pdb
PDB entry 6fas coloured by chain, front view.
PDB entry 6fas coloured by chain, side view.
PDB entry 6fas coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
Sasnauskas G, Kauneckaite K, Siksnys V
Nucleic Acids Res 46 4316-4324 (2018)
PMID: 29660015

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119882 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
B3 domain-containing transcription repressor VAL1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8W4L5 (Residues: 287-397; Coverage: 14%)
Gene names: At2g30470, HSI2, T6B20.17, VAL1
Sequence domains: B3 DNA binding domain
Structure domains: DNA-binding pseudobarrel domain
DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 12 nucleotides
Theoretical weight: 3.63 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand CME 2 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P21
Unit cell:
a: 40.091Å b: 86.577Å c: 65.16Å
α: 90° β: 94.14° γ: 90°
R-values:
R R work R free
0.174 0.17 0.217
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants.
Baile et al. (2022)
2 more

2 mentions without citation

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
Sasnauskas et al. (2018)
1 more