Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 2 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 73629.69 
• Atom Count: 4811 
• Residue Count: 576 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1H9D

Aml1/cbf-beta/dna complex

• DOI: 10.2210/pdb1H9D/pdb
• NDB: PD0210

• Classification: TRANSCRIPTION FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2001-03-07 Released: 2001-03-31 
• Deposition Author(s): Bravo, J., Warren, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.271 
• R-Value Work: 0.237 

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.Mol.Biol. 8: 371

• PubMed: 11276260 
• DOI: 10.1038/86264


• 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. 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.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CORE-BINDING FACTOR ALPHA SUBUNIT1	A, C	134	Homo sapiens	Mutation(s): 0  Gene Names: RUNX1 (AML1, CBFA2)
Find proteins for Q01196 (Homo sapiens) Go to Gene View: RUNX1 Go to UniProtKB:  Q01196

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
CORE-BINDING FACTOR CBF-BETA	B, D	134	Homo sapiens	Mutation(s): 0  Gene Names: CBFB
Find proteins for Q13951 (Homo sapiens) Go to Gene View: CBFB Go to UniProtKB:  Q13951

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')	E,G	10	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')	F,H	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.271 
• R-Value Work: 0.237 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 115.033	α = 90.00
b = 115.033	β = 90.00
c = 133.925	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CNS	refinement
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-07 
• Released Date: 2001-03-31 
• Deposition Author(s): Bravo, J., Warren, A.J.

Revision History 

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