Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2BC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65658.31 
• Atom Count: 4189 
• Residue Count: 472 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

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

• DOI: 10.2210/pdb1IO4/pdb
• NDB: PD0198

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2001-01-10 Released: 2001-03-12 
• Deposition Author(s): Tahirov, T.H., Ogata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.299 
• R-Value Work: 0.247 

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

• PubMed: 11257229 
• Primary Citation of Related Structures:  
  1HJC, 1HJB
• Also Cited By: 1H8A, 1H89, 1GU5, 1GU4, 1GTW


• 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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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 --: --




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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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
CAAT/ENHANCER BINDING PROTEIN BETA	A, B	78	Homo sapiens	Mutation(s): 0  Gene Names: CEBPB (TCF5)
Find proteins for P17676 (Homo sapiens) Go to Gene View: CEBPB Go to UniProtKB:  P17676

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
RUNT-RELATED TRANSCRIPTION FACTOR 1	C	123	Mus musculus	Mutation(s): 0  Gene Names: Runx1 (Aml1, Cbfa2, Pebp2ab)
Find proteins for Q03347 (Mus musculus) Go to UniProtKB:  Q03347

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
CORE-BINDING FACTOR, BETA SUBUNIT	D	141	Mus musculus	Mutation(s): 0  Gene Names: Cbfb (Pebp2b, Pebpb2)
Find proteins for Q08024 (Mus musculus) Go to UniProtKB:  Q08024

Entity ID: 1
Molecule	Chains	Length	Organism
CSF-1R PROMOTER	E	26	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
CSF-1R PROMOTER	F	26	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
AU	C, D	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.299 
• R-Value Work: 0.247 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 121.108	α = 90.00
b = 163.600	β = 90.00
c = 109.326	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-10 
• Released Date: 2001-03-12 
• Deposition Author(s): Tahirov, T.H., Ogata, K.

Revision History 

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