1HJB

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

• PDB DOI: https://doi.org/10.2210/pdb1HJB/pdb
• NAKB: 1HJB

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-01-11 Released: 2001-03-09 
• Deposition Author(s): Tahirov, T.H., Ogata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.313 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 

Starting Model: experimental

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

• PubMed: 11257229 
• DOI: https://doi.org/10.1016/s0092-8674(01)00271-9
• Primary Citation of 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.

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Organizational Affiliation: 

Kanagawa Academy of Science and Technology (KAST), Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama 236-0004, Kanazawa-ku, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CCAAT/ENHANCER BINDING PROTEIN BETA	A, B, D, E	87	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RUNT-RELATED TRANSCRIPTION FACTOR 1	C, F	123	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q03347 (Mus musculus) Explore Q03347  Go to UniProtKB:  Q03347

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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	26	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
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	26	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.313 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.165	α = 90
b = 109.273	β = 90
c = 127.405	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-09 
Deposition Author(s): Tahirov, T.H., Ogata, K.

Revision History  

• 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