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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription Regulator NC2 alpha chainC [auth A]98Homo sapiensMutation(s): 0 
Gene Names: NC2 alpha (DRAP1)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14919 (Homo sapiens)
Explore Q14919 
Go to UniProtKB:  Q14919
PHAROS:  Q14919
GTEx:  ENSG00000175550 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14919
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription Regulator NC2 beta chainD [auth B]179Homo sapiensMutation(s): 0 
Gene Names: NC2 beta (Dr1)
UniProt & NIH Common Fund Data Resources
Find proteins for Q01658 (Homo sapiens)
Explore Q01658 
Go to UniProtKB:  Q01658
PHAROS:  Q01658
GTEx:  ENSG00000117505 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01658
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-BOX-BINDING PROTEIN (TBP)E [auth C]185Homo sapiensMutation(s): 0 
Gene Names: tbp
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
PHAROS:  P20226
GTEx:  ENSG00000112592 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20226
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
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
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
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
Sequence Annotations
Expand
  • Reference Sequence
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 

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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description