1JFI

Crystal Structure of the NC2-TBP-DNA Ternary Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.

Kamada, K.Shu, F.Chen, H.Malik, S.Stelzer, G.Roeder, R.G.Meisterernst, M.Burley, S.K.

(2001) Cell 106: 71-81

  • DOI: 10.1016/s0092-8674(01)00417-2
  • Primary Citation of Related Structures:  
    1JFI

  • PubMed Abstract: 
  • The X-ray structure of a ternary complex of Negative Cofactor 2 (NC2), the TATA box binding protein (TBP), and DNA has been determined at 2.6 A resolution. The N termini of NC2 alpha and beta resemble histones H2A and H2B, respectively, and form a he ...

    The X-ray structure of a ternary complex of Negative Cofactor 2 (NC2), the TATA box binding protein (TBP), and DNA has been determined at 2.6 A resolution. The N termini of NC2 alpha and beta resemble histones H2A and H2B, respectively, and form a heterodimer that binds to the bent DNA double helix on the underside of the preformed TBP-DNA complex via electrostatic interactions. NC2beta contributes to inhibition of TATA-dependent transcription through interactions of its C-terminal alpha helix with a conserved hydrophobic feature on the upper surface of TBP, which in turn positions the penultimate alpha helix of NC2beta to block recognition of the TBP-DNA complex by transcription factor IIB. Further regulatory implications of the NC2 heterodimer structure are discussed.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, 1230 York Avenue, New York, NY 10021, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription Regulator NC2 alpha chainA98Homo sapiensMutation(s): 0 
Gene Names: NC2 alpha (DRAP1)DRAP1
Find proteins for Q14919 (Homo sapiens)
Explore Q14919 
Go to UniProtKB:  Q14919
NIH Common Fund Data Resources
PHAROS  Q14919
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription Regulator NC2 beta chainB179Homo sapiensMutation(s): 0 
Gene Names: NC2 beta (Dr1)DR1
Find proteins for Q01658 (Homo sapiens)
Explore Q01658 
Go to UniProtKB:  Q01658
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PHAROS  Q01658
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-BOX-BINDING PROTEIN (TBP)C185Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
NIH Common Fund Data Resources
PHAROS  P20226
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP*C)-3'D19N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP*A)-3'E19N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.62 Å
      • R-Value Free: 0.277 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.236 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 76.684α = 90
      b = 119.075β = 90
      c = 155.076γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2001-07-11
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance