5T1J

Crystal Structure of the Tbox DNA binding domain of the transcription factor T-bet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.947 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.

Liu, C.F.Brandt, G.S.Hoang, Q.Q.Naumova, N.Lazarevic, V.Hwang, E.S.Dekker, J.Glimcher, L.H.Ringe, D.Petsko, G.A.

(2016) Proc.Natl.Acad.Sci.USA 113: E6572-E6581

  • DOI: 10.1073/pnas.1613914113

  • PubMed Abstract: 
  • The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the T <sub>H </sub>1 response ...

    The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the T H 1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. The data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.


    Organizational Affiliation

    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115; Division of Rheumatology, Allergy, and Immunology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; Ragon Institute of Massachusetts Institute of Technology, Massachusetts General Hospital, and Harvard University, Charlestown, MA 02129.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115.,Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10021; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; cel2010@med.cornell.edu gpetsko@med.cornell.edu.,Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; Department of Chemistry, Franklin and Marshall College, Lancaster, PA 17604.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115; Division of Life and Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-box transcription factor TBX21
A, B
204Mus musculusMutation(s): 0 
Gene Names: Tbx21 (Tbet, Tblym)
Find proteins for Q9JKD8 (Mus musculus)
Go to UniProtKB:  Q9JKD8
Entity ID: 2
MoleculeChainsLengthOrganism
DNAC,D,E,F24synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.947 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.266 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 70.450α = 90.00
b = 70.450β = 90.00
c = 438.389γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
Blu-Icedata collection
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description