DNA recognition is mediated by conformational transition and by DNA bending

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


DNA Recognition by the RUNX1 Transcription Factor Is Mediated by an Allosteric Transition in the RUNT Domain and by DNA Bending.

Bartfeld, D.Shimon, L.Couture, G.Rabinovich, D.Frolow, F.Levanon, D.Groner, Y.Shakked, Z.

(null) Structure 10: 1395-1407

  • DOI: https://doi.org/10.1016/s0969-2126(02)00853-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Runt domain proteins are transcription regulators of major developmental pathways. Here we present the crystal structures of the Runt domain (RD) of the human protein RUNX1 and its DNA binding site in their free states and compare them with the published crystal structures of RD bound to DNA and to the partner protein CBFbeta. We demonstrate that (1) RD undergoes an allosteric transition upon DNA binding, which is further stabilized by CBFbeta, and that (2) the free DNA target adopts a bent-helical conformation compatible with that of the complex. These findings elucidate the mechanism by which CBFbeta enhances RD binding to DNA as well as the role of the intrinsic conformation of the DNA target in the recognition process.

  • Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RUNX1 transcription factor
A, B
131Homo sapiensMutation(s): 0 
Gene Names: human
UniProt & NIH Common Fund Data Resources
Find proteins for Q01196 (Homo sapiens)
Explore Q01196 
Go to UniProtKB:  Q01196
PHAROS:  Q01196
GTEx:  ENSG00000159216 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01196
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.23α = 90
b = 121.23β = 90
c = 186.33γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MTF/ULTIMAmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description