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 

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


  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcription Regulator NC2 alpha chain
A
98Homo sapiensMutation(s): 0 
Gene Names: DRAP1
Find proteins for Q14919 (Homo sapiens)
Go to Gene View: DRAP1
Go to UniProtKB:  Q14919
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Transcription Regulator NC2 beta chain
B
179Homo sapiensMutation(s): 0 
Gene Names: DR1
Find proteins for Q01658 (Homo sapiens)
Go to Gene View: DR1
Go to UniProtKB:  Q01658
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
TATA-BOX-BINDING PROTEIN (TBP)
C
185Homo sapiensMutation(s): 0 
Gene Names: TBP (GTF2D1, TF2D, TFIID)
Find proteins for P20226 (Homo sapiens)
Go to Gene View: TBP
Go to UniProtKB:  P20226
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP*C)-3'D19N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.684α = 90.00
b = 119.075β = 90.00
c = 155.076γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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