1H9D

Aml1/cbf-beta/dna complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Leukemia-Associated Aml1 (Runx1)-Cbfbeta Complex Functions as a DNA-Induced Molecular Clamp

Bravo, J.Li, Z.Speck, N.A.Warren, A.J.

(2001) Nat.Struct.Mol.Biol. 8: 371

  • DOI: 10.1038/86264

  • PubMed Abstract: 
  • We have determined the structure, at 2.6 A resolution, of the AML1 (Runx1) Runt domain--CBF beta--DNA ternary complex, the most common target for mutations in human leukemia. The structure reveals that the Runt domain DNA binding mechanism is unique ...

    We have determined the structure, at 2.6 A resolution, of the AML1 (Runx1) Runt domain--CBF beta--DNA ternary complex, the most common target for mutations in human leukemia. The structure reveals that the Runt domain DNA binding mechanism is unique within the p53 family of transcription factors. The extended C-terminal 'tail' and 'wing' elements adopt a specific DNA-bound conformation that clamps the phosphate backbone between the major and minor grooves of the distorted B-form DNA recognition site. Furthermore, the extended 'tail' mediates most of the NF-kappa B/Rel-like base-specific contacts in the major groove. The structure clearly explains the molecular basis for the loss of DNA binding function of the Runt domain--CBF beta complex as a consequence of the human disease-associated mutations in leukemogenesis and cleidocranial dysplasia.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CORE-BINDING FACTOR ALPHA SUBUNIT1
A, C
134Homo sapiensMutation(s): 0 
Gene Names: RUNX1 (AML1, CBFA2)
Find proteins for Q01196 (Homo sapiens)
Go to Gene View: RUNX1
Go to UniProtKB:  Q01196
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CORE-BINDING FACTOR CBF-BETA
B, D
134Homo sapiensMutation(s): 0 
Gene Names: CBFB
Find proteins for Q13951 (Homo sapiens)
Go to Gene View: CBFB
Go to UniProtKB:  Q13951
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')E,G10N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')F,H10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.033α = 90.00
b = 115.033β = 90.00
c = 133.925γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-31
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Advisory, Source and taxonomy