› 5yzy

X-ray diffraction
2.61Å resolution

AtVAL1 B3 domain in complex with 13bp-DNA

Released:
DOI: 10.2210/pdb5yzy/pdb
PDB entry 5yzy coloured by chain, front view.
PDB entry 5yzy coloured by chain, side view.
PDB entry 5yzy coloured by chain, top view.
Source organisms:
Primary publication:
Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
Wu B, Zhang M, Su S, Liu H, Gan J, Ma J
Biochem Biophys Res Commun 501 415-422 (2018)
PMID: 29733847

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-119472 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
B3 domain-containing transcription repressor VAL1 Chain: C
Molecule details ›
Chain: C
Length: 128 amino acids
Theoretical weight: 14.19 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8W4L5 (Residues: 273-400; Coverage: 16%)
Gene names: At2g30470, HSI2, T6B20.17, VAL1
Sequence domains: B3 DNA binding domain
Structure domains: DNA-binding pseudobarrel domain
DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand HG 1 x HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: I4122
Unit cell:
a: 87.78Å b: 87.78Å c: 148.735Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants.
Baile et al. (2022)
7 other articles

1 mention without citation

In silico predictions on the possible mechanism of action of selected bioactive compounds against breast cancer.
Muhammad et al. (2020)