1IO4

CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta.

Tahirov, T.H.Inoue-Bungo, T.Morii, H.Fujikawa, A.Sasaki, M.Kimura, K.Shiina, M.Sato, K.Kumasaka, T.Yamamoto, M.Ishii, S.Ogata, K.

(2001) Cell 104: 755-767

  • DOI: 10.1016/s0092-8674(01)00271-9
  • Primary Citation of Related Structures:  
    1HJC, 1HJB, 1IO4

  • PubMed Abstract: 
  • The core binding factor (CBF) heterodimeric transcription factors comprised of AML/CBFA/PEBP2alpha/Runx and CBFbeta/PEBP2beta subunits are essential for differentiation of hematopoietic and bone cells, and their mutation is intimately related to the development of acute leukemias and cleidocranial dysplasia ...

    The core binding factor (CBF) heterodimeric transcription factors comprised of AML/CBFA/PEBP2alpha/Runx and CBFbeta/PEBP2beta subunits are essential for differentiation of hematopoietic and bone cells, and their mutation is intimately related to the development of acute leukemias and cleidocranial dysplasia. Here, we present the crystal structures of the AML1/Runx-1/CBFalpha(Runt domain)-CBFbeta(core domain)-C/EBPbeta(bZip)-DNA, AML1/Runx-1/CBFalpha(Runt domain)-C/EBPbeta(bZip)-DNA, and AML1/Runx-1/CBFalpha(Runt domain)-DNA complexes. The hydrogen bonding network formed among CBFalpha(Runt domain) and CBFbeta, and CBFalpha(Runt domain) and DNA revealed the allosteric regulation mechanism of CBFalpha(Runt domain)-DNA binding by CBFbeta. The point mutations of CBFalpha related to the aforementioned diseases were also mapped and their effect on DNA binding is discussed.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analyses of Quaternary, Ternary and Binary Protein-DNA Complexes with Involvement of AML1/Runx-1/Cbfalpha Runt Domain, Cbfbeta and the C/EBPbeta bZIP Region
      Tahirov, T.H., Inoue, T., Sasaki, M., Shiina, M., Kimura, K., Sato, K., Kumasaka, T., Yamamoto, M., Kamiya, N., Ogata, K.
      () To be published --: --

    Organizational Affiliation

    Kanagawa Academy of Science and Technology (KAST), Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama 236-0004, Kanazawa-ku, Japan. tahir@med.yokohama-cu.ac.jp



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CAAT/ENHANCER BINDING PROTEIN BETA AB78Homo sapiensMutation(s): 0 
Gene Names: CEBPBTCF5PP9092
Find proteins for P17676 (Homo sapiens)
Explore P17676 
Go to UniProtKB:  P17676
NIH Common Fund Data Resources
PHAROS:  P17676
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RUNT-RELATED TRANSCRIPTION FACTOR 1 C123Mus musculusMutation(s): 0 
Gene Names: Runx1Aml1Cbfa2Pebp2ab
Find proteins for Q03347 (Mus musculus)
Explore Q03347 
Go to UniProtKB:  Q03347
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
CORE-BINDING FACTOR, BETA SUBUNIT D141Mus musculusMutation(s): 0 
Gene Names: CbfbPebp2bPebpb2
Find proteins for Q08024 (Mus musculus)
Explore Q08024 
Go to UniProtKB:  Q08024
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
CSF-1R PROMOTERE26N/A
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
CSF-1R PROMOTERF26N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AU
Query on AU

Download Ideal Coordinates CCD File 
C, D
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.108α = 90
b = 163.6β = 90
c = 109.326γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance