› 5z00

X-ray diffraction
2.59Å resolution

AtVAL1 B3 domain in complex with 15bp-DNA

Released:
DOI: 10.2210/pdb5z00/pdb
PDB entry 5z00 coloured by chain, front view.
PDB entry 5z00 coloured by chain, side view.
PDB entry 5z00 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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119474 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
B3 domain-containing transcription repressor VAL1 Chains: C, G, K, M
Molecule details ›
Chains: C, G, K, M
Length: 128 amino acids
Theoretical weight: 14.19 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
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*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3') Chains: A, E, I
Molecule details ›
Chains: A, E, I
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3') Chains: B, J
Molecule details ›
Chains: B, J
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*T)-3') Chain: F
Molecule details ›
Chain: F
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 68.223Å b: 97.416Å c: 71.149Å
α: 90° β: 110.19° γ: 90°
R-values:
R R work R free
0.219 0.216 0.268
Expression systems:
  • Arabidopsis thaliana
  • 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