Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

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

Macromolecule Content

• Total Structure Weight: 50223.77 
• Atom Count: 3105 
• Residue Count: 336 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1H8A

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3

• DOI: 10.2210/pdb1H8A/pdb
• NDB: PD0290

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, Avian myeloblastosis virus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2001-01-31 Released: 2002-01-28 
• Deposition Author(s): Tahirov, T.H., Ogata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.288 
• R-Value Work: 0.245 

Literature

Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter

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

(2002) Cell 108: 57

• PubMed: 11792321 
• Primary Citation of Related Structures:  
  1H89, 1H88
• Also Cited By: 1GV2, 1GVD, 1GV5, 1GUU, 1GU5, 1GU4, 1GTW


• PubMed Abstract: 
  

c-Myb, but not avian myeloblastosis virus (AMV) v-Myb, cooperates with C/EBP beta to regulate transcription of myeloid-specific genes. To assess the structural basis for that difference, we determined the crystal structures of complexes comprised of the c-Myb or AMV v-Myb DNA-binding domain (DBD), the C/EBP beta DBD, and a promoter DNA fragment. Within the c-Myb complex, a DNA-bound C/EBP beta interacts with R2 of c-Myb bound to a different DNA fragment; point mutations in v-Myb R2 eliminate such interaction within the v-Myb complex. GST pull-down assays, luciferase trans-activation assays, and atomic force microscopy confirmed that the interaction of c-Myb and C/EBP beta observed in crystal mimics their long range interaction on the promoter, which is accompanied by intervening DNA looping.

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Related Citations: 

• Crystals of Ternary Protein-DNA Complexes Composed of DNA-Binding Domains C-Myb or V-Myb, C/Ebpalpha or C/Ebpbeta and Tom-1A Promoter Fragment
  Tahirov, T.H.,Inoue, T.,Sasaki, M.,Shiina, M.,Kimura, K.,Sato, K.,Kumasaka, T.,Yamamoto, M.,Kamiya, N.,Ogata, K.
  (2001) Acta Crystallogr.,Sect.D 57: 1655
• 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
• Crystal Structures of C-Myb DNA-Binding Domain in Free State: An Evidence for Binding of Na+ and Comparison with Solution Structure
  Tahirov, T.H.,Morii, H.,Uedaira, H.,Sasaki, M.,Sarai, A.,Adachi, S.,Park, S.Y.,Kamiya, N.,Ogata, K.
  () TO BE PUBLISHED --: --




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Organizational Affiliation: 

Kanagawa Academy of Science and Technology, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
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: 2
Molecule	Chains	Sequence Length	Organism	Details
MYB TRANSFORMING PROTEIN	C	128	Avian myeloblastosis virus	Mutation(s): 0  Gene Names: V-MYB
Find proteins for P01104 (Avian myeloblastosis virus) Go to UniProtKB:  P01104

Entity ID: 3
Molecule	Chains	Length	Organism
DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3')	D	26	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3')	E	26	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.288 
• R-Value Work: 0.245 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 109.860	α = 90.00
b = 166.700	β = 90.00
c = 39.600	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-31 
• Released Date: 2002-01-28 
• Deposition Author(s): Tahirov, T.H., Ogata, K.

Revision History 

• Version 1.0: 2002-01-28
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance