1XBR

T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor.

Muller, C.W.Herrmann, B.G.

(1997) Nature 389: 884-888

  • DOI: 10.1038/39929
  • Also Cited By: 1H6F

  • PubMed Abstract: 
  • The mouse Brachyury (T) gene is the prototype of a growing family of so-called T-box genes which encode transcriptional regulators and have been identified in a variety of invertebrates and vertebrates, including humans. Mutations in Brachyury and ot ...

    The mouse Brachyury (T) gene is the prototype of a growing family of so-called T-box genes which encode transcriptional regulators and have been identified in a variety of invertebrates and vertebrates, including humans. Mutations in Brachyury and other T-box genes result in drastic embryonic phenotypes, indicating that T-box gene products are essential in tissue specification, morphogenesis and organogenesis. The T-box encodes a DNA-binding domain of about 180 amino-acid residues, the T domain. Here we report the X-ray structure of the T domain from Xenopus laevis in complex with a 24-nucleotide palindromic DNA duplex. We show that the protein is bound as a dimer, interacting with the major and the minor grooves of the DNA. A new type of specific DNA contact is seen, in which a carboxy-terminal helix is deeply embedded into an enlarged minor groove without bending the DNA. Hydrophobic interactions and an unusual main-chain carbonyl contact to a guanine account for sequence-specific recognition in the minor groove by this helix. Thus the structure of this T domain complex with DNA reveals a new way in which a protein can recognize DNA.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, France. mueller@embl-grenoble.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (T PROTEIN)
A, B
184Xenopus laevisMutation(s): 0 
Gene Names: tbxt (bra, t)
Find proteins for P24781 (Xenopus laevis)
Go to UniProtKB:  P24781
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP* TP*T)-3')C,D24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.900α = 90.00
b = 113.900β = 90.00
c = 149.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CCP4model building
X-PLORrefinement
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-07-16 
  • Released Date: 1998-01-16 
  • Deposition Author(s): Muller, C.W.

Revision History 

  • Version 1.0: 1998-01-16
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance