1AU7

PIT-1 MUTANT/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility.

Jacobson, E.M.Li, P.Leon-del-Rio, A.Rosenfeld, M.G.Aggarwal, A.K.

(1997) Genes Dev. 11: 198-212


  • PubMed Abstract: 
  • Pit-1, a member of the POU domain family of transcription factors, characterized by a bipartite DNA-binding domain, serves critical developmental functions based on binding to diverse DNA elements in its target genes. Here we report a high resolution ...

    Pit-1, a member of the POU domain family of transcription factors, characterized by a bipartite DNA-binding domain, serves critical developmental functions based on binding to diverse DNA elements in its target genes. Here we report a high resolution X-ray analysis of the Pit-1 POU domain bound to a DNA element as a homodimer. This analysis reveals that Pit-1 subdomains bind to perpendicular faces of the DNA, rather than opposite faces of the DNA as in Oct-1. This is accomplished by different spacing and orientation of the POU-specific domain. Contrary to previous predictions, the dimerization interface involves the carboxyl terminus of the DNA recognition helix of the homeodomain, which in an extended conformation interacts with specific residues at the amino terminus of helix alpha1 and in the loop between helices alpha3 and alpha4 of the POU-specific domain of the symmetry related monomer. These features suggest the molecular basis of disease-causing mutations in Pit-1 and provide potential basis for the flexible allostery between protein domains and DNA sites in the activation of target genes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN PIT-1
A, B
146Rattus norvegicusGene Names: Pou1f1 (Ghf-1, Pit-1, Pit1)
Find proteins for P10037 (Rattus norvegicus)
Go to UniProtKB:  P10037
Entity ID: 1
MoleculeChainsLengthOrganism
CONSENSUS DNA 25-MERC25N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*CP*CP*TP*CP*AP*TP*GP*TP*AP*TP*AP*TP*AP*C P*AP*TP*GP*AP*GP* GP*A)-3')D24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.230 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.500α = 76.70
b = 50.100β = 79.30
c = 55.800γ = 67.20
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
PHASITphasing
PHASITmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance