1HJB | pdb_00001hjb

CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN 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: 
    0.313 (Depositor) 
  • R-Value Work: 
    0.244 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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

  • DOI: https://doi.org/10.1016/s0092-8674(01)00271-9
  • Primary Citation Related Structures: 
    1HJB, 1HJC, 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. 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.

    • 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

Macromolecule Content 

  • Total Structure Weight: 100.38 kDa 
  • Atom Count: 6,270 
  • Modeled Residue Count: 613 
  • Deposited Residue Count: 698 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CCAAT/ENHANCER BINDING PROTEIN BETA
A, B, D, E
87Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P17676 (Homo sapiens)
Explore P17676 
Go to UniProtKB:  P17676
PHAROS:  P17676
GTEx:  ENSG00000172216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17676
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RUNT-RELATED TRANSCRIPTION FACTOR 1
C, F
123Mus musculusMutation(s): 0 
UniProt
Find proteins for Q03347 (Mus musculus)
Explore Q03347 
Go to UniProtKB:  Q03347
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03347
Sequence Annotations
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Reference Sequence
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(by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3')
G, I
26Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3')
H, J
26Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.313 (Depositor) 
  • R-Value Work:  0.244 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.165α = 90
b = 109.273β = 90
c = 127.405γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-09
    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: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description