1H8A

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • Primary Citation of Related Structures:  
  • 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 ...

    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.


    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 --: --


    Organizational Affiliation

    Kanagawa Academy of Science and Technology, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan. tahir@med.yokohama-cu.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAAT/ENHANCER BINDING PROTEIN BETA
A, B
78Homo sapiensMutation(s): 0 
Gene Names: CEBPB (TCF5)
Find proteins for P17676 (Homo sapiens)
Go to Gene View: CEBPB
Go to UniProtKB:  P17676
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MYB TRANSFORMING PROTEIN
C
128Avian myeloblastosis virusMutation(s): 0 
Gene Names: V-MYB
Find proteins for P01104 (Avian myeloblastosis virus)
Go to UniProtKB:  P01104
Entity ID: 3
MoleculeChainsLengthOrganism
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')D26N/A
Entity ID: 4
MoleculeChainsLengthOrganism
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')E26N/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 = 109.860α = 90.00
b = 166.700β = 90.00
c = 39.600γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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