1AU7

PIT-1 MUTANT/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.230 

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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

  • DOI: 10.1101/gad.11.2.198
  • Primary Citation of Related Structures:  
    1AU7

  • 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 X-ray analysis of the Pit-1 POU domain bound to a DNA element as a homodimer ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN PIT-1C [auth A], D [auth B]146Rattus norvegicusMutation(s): 2 
Gene Names: Pit-1Pou1f1Ghf-1Pit1
UniProt
Find proteins for P10037 (Rattus norvegicus)
Explore P10037 
Go to UniProtKB:  P10037
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
CONSENSUS DNA 25-MERA [auth C]25N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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')B [auth D]24N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.230 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.5α = 76.7
b = 50.1β = 79.3
c = 55.8γ = 67.2
Software Package:
Software NamePurpose
PHASITmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASITphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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