1H9D

Aml1/cbf-beta/dna complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 
  • R-Value Observed: 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 Biol 8: 371

  • DOI: 10.1038/86264
  • Primary Citation of Related Structures:  
    1H9D

  • 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 within the p53 family of transcription factors ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CORE-BINDING FACTOR ALPHA SUBUNIT1 AC134Homo sapiensMutation(s): 0 
Gene Names: AML1RUNX1CBFA2
Find proteins for Q01196 (Homo sapiens)
Explore Q01196 
Go to UniProtKB:  Q01196
NIH Common Fund Data Resources
PHAROS:  Q01196
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CORE-BINDING FACTOR CBF-BETA BD134Homo sapiensMutation(s): 0 
Gene Names: CBFB
Find proteins for Q13951 (Homo sapiens)
Explore Q13951 
Go to UniProtKB:  Q13951
NIH Common Fund Data Resources
PHAROS:  Q13951
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')E, G10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')F, H10N/A
      Small Molecules
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      DNAKd :  0.010000000707805157   nM  PDBBind
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.60 Å
      • R-Value Free: 0.271 
      • R-Value Work: 0.237 
      • R-Value Observed: 0.237 
      • Space Group: P 43 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 115.033α = 90
      b = 115.033β = 90
      c = 133.925γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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