Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26719.07 
• Atom Count: 1722 
• Residue Count: 164 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1UBD

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

• DOI: 10.2210/pdb1UBD/pdb
• NDB: PDT038

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 1996-10-04 Released: 1996-12-23 
• Deposition Author(s): Houbaviy, H.B., Usheva, A., Shenk, T., Burley, S.K.

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Experimental Data Snapshot

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

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: 8942976 


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (YY1 ZINC FINGER DOMAIN)	C	124	Homo sapiens	Mutation(s): 2  Gene Names: YY1 (INO80S)
Find proteins for P25490 (Homo sapiens) Go to Gene View: YY1 Go to UniProtKB:  P25490

Entity ID: 1
Molecule	Chains	Length	Organism
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')	A	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
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')	B	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 44.000	α = 90.00
b = 65.700	β = 90.00
c = 117.100	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-10-04 
• Released Date: 1996-12-23 
• Deposition Author(s): Houbaviy, H.B., Usheva, A., Shenk, T., Burley, S.K.

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