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 

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This is version 1.3 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 heterodimer that binds to the bent DNA double helix on the underside of the preformed TBP-DNA complex via electrostatic interactions ...

    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 chainC [auth A]98Homo sapiensMutation(s): 0 
Gene Names: NC2 alpha (DRAP1)DRAP1
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Find proteins for Q14919 (Homo sapiens)
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Go to UniProtKB:  Q14919
PHAROS:  Q14919
GTEx:  ENSG00000175550 
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UniProt GroupQ14919
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription Regulator NC2 beta chainD [auth B]179Homo sapiensMutation(s): 0 
Gene Names: NC2 beta (Dr1)DR1
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Find proteins for Q01658 (Homo sapiens)
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Go to UniProtKB:  Q01658
PHAROS:  Q01658
GTEx:  ENSG00000117505 
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UniProt GroupQ01658
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-BOX-BINDING PROTEIN (TBP)E [auth C]185Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
PHAROS:  P20226
GTEx:  ENSG00000112592 
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UniProt GroupP20226
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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'A [auth D]19N/A
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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'B [auth E]19N/A
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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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-02-03
    Changes: Database references, Structure summary