1UBD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.

Houbaviy, H.B.Usheva, A.Shenk, T.Burley, S.K.

(1996) Proc.Natl.Acad.Sci.USA 93: 13577-13582


  • PubMed Abstract: 
  • Ying-Yang 1 protein (YY1) supports specific, unidirectional initiation of messenger RNA production by RNA polymerase II from two adjacent start sites in the adeno-associated virus P5 promoter, a process which is independent of the TATA box-binding pr ...

    Ying-Yang 1 protein (YY1) supports specific, unidirectional initiation of messenger RNA production by RNA polymerase II from two adjacent start sites in the adeno-associated virus P5 promoter, a process which is independent of the TATA box-binding protein (TBP). The 2.5-A resolution YY1-initiator element cocrystal structure reveals four zinc fingers recognizing a YY1-binding consensus sequence. Upstream of the transcription start sites protein-DNA contacts involve both strands and downstream they are virtually restricted to the template strand, permitting access to the active center of RNA polymerase II and ensuring specificity and directionality. The observed pattern of protein-DNA contacts also explains YY1 binding to a preformed transcription bubble, and YY1 binding to a DNA/RNA hybrid analog of the P5 promoter region containing a nascent RNA transcript. A model is proposed for YY1-directed, TBP-independent transcription initiation.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, Rockefeller University, New York, NY 10021-6399, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (YY1 ZINC FINGER DOMAIN)
C
124Homo sapiensMutation(s): 2 
Gene Names: YY1 (INO80S)
Find proteins for P25490 (Homo sapiens)
Go to Gene View: YY1
Go to UniProtKB:  P25490
Entity ID: 1
MoleculeChainsLengthOrganism
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')A20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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')B20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.000α = 90.00
b = 65.700β = 90.00
c = 117.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance