1H6F

Human TBX3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the DNA-Bound T-Box Domain of Human Tbx3, a Transcription Factor Responsible for Ulnar- Mammary Syndrome

Coll, M.Seidman, J.G.Muller, C.W.

(2002) Structure 10: 343

  • DOI: 10.1016/s0969-2126(02)00722-0
  • Primary Citation of Related Structures:  
    1H6F

  • PubMed Abstract: 
  • T-box genes encode transcription factors involved in morphogenesis and organogenesis of vertebrates and invertebrates. Mutations in human T-box genes TBX3, TBX5, and TBX1 cause severe genetic disorders known as Ulnar-Mammary syndrome (UMS), Holt-Oram syndrome (HOS), and DiGeorge syndrome, respectively ...

    T-box genes encode transcription factors involved in morphogenesis and organogenesis of vertebrates and invertebrates. Mutations in human T-box genes TBX3, TBX5, and TBX1 cause severe genetic disorders known as Ulnar-Mammary syndrome (UMS), Holt-Oram syndrome (HOS), and DiGeorge syndrome, respectively. The crystal structure of the T-box domain of the first human T-box transcription factor, TBX3, in complex with DNA at 1.7 A resolution explains structural consequences of T-box domain point mutations observed in UMS and HOS patients. Comparison with the structure of the T-box domain from Xenopus laevis (Xbra) bound to DNA shows differences in several secondary structure elements and in the quaternary structure of the two complexes. TBX3 independently recognizes the two binding sites present in the palindromic DNA duplex, whereas in Xbra, binding to the palindrome is stabilized through interactions between the two monomers. The different quaternary structures suggest different DNA binding modes for T-box transcription factors.


    Related Citations: 
    • Crystallographic Structure of the T Domain-DNA Complex of the Brachyury Transcription Factor
      Muller, C.W., Hermann, B.
      (1997) Nature 389: 880

    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-BOX TRANSCRIPTION FACTOR TBX3A, B193Homo sapiensMutation(s): 0 
Gene Names: TBX3
UniProt & NIH Common Fund Data Resources
Find proteins for O15119 (Homo sapiens)
Explore O15119 
Go to UniProtKB:  O15119
PHAROS:  O15119
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'C, D24synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.04α = 90
b = 104.91β = 90
c = 125.31γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2001-06-13 
  • Released Date: 2002-04-19 
  • Deposition Author(s): Coll, M., Muller, C.W.

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-28
    Changes: Advisory, Source and taxonomy, Structure summary