› 1ubd

X-ray diffraction
2.5Å resolution

CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT

Released:
DOI: 10.2210/pdb1ubd/pdb
PDB entry 1ubd coloured by chain, front view.
PDB entry 1ubd coloured by chain, side view.
PDB entry 1ubd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.
Houbaviy HB, Usheva A, Shenk T, Burley SK
Proc Natl Acad Sci U S A 93 13577-82 (1996)
PMID: 8942976

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114696 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional repressor protein YY1 Chain: C
Molecule details ›
Chain: C
Length: 124 amino acids
Theoretical weight: 14.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P25490 (Residues: 291-414; Coverage: 30%)
Gene names: INO80S, YY1
Sequence domains: Zinc finger, C2H2 type
Structure domains: Classic Zinc Finger
DNA (5'-D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*A P*GP*CP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 20 nucleotides
Theoretical weight: 6.16 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*GP*CP*TP*TP*CP*AP*AP*AP*AP*TP*GP*GP*AP*GP*AP*C P*CP*CP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.1 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P212121
Unit cell:
a: 44Å b: 65.7Å c: 117.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.33
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

26 review citations

Genome editing with engineered zinc finger nucleases.
Urnov et al. (2010)
25 more

34 mentions without citation

The Two Sides of YY1 in Cancer: A Friend and a Foe.
Sarvagalla et al. (2019)
33 more