1H89

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • DOI: 10.1016/s0092-8674(01)00636-5
  • Structures With Same Primary Citation

  • 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 D Biol Crystallogr 57: 1655
    • Crystal Structures of C-Myb DNA-Binding Domain in Free State: An Evidence for Binding of Na+ and Comparison with Solution Structure Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region
      Tahirov, T.H., Morii, H., Uedaira, H., Sasaki, M., Sarai, A., Adachi, S., Park, S.Y., Kamiya, N., Ogata, K.
      () To be published --: --
    • 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

    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
64Homo sapiensMutation(s): 0 
Gene Names: CEBPBTCF5PP9092
Find proteins for P17676 (Homo sapiens)
Go to UniProtKB:  P17676
NIH Common Fund Data Resources
PHAROS  P17676

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MYB PROTO-ONCOGENE PROTEIN
C
159Mus musculusMutation(s): 2 
Gene Names: Myb
Find proteins for P06876 (Mus musculus)
Go to UniProtKB:  P06876
NIH Common Fund Data Resources
IMPC  MGI:97249

Find similar nucleic acids by: Sequence  |  Structure

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')D26Homo sapiens

Find similar nucleic acids by: Sequence  |  Structure

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')E26Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download CCD File 
C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd :  1.6399999856948853   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.684α = 90
b = 73.383β = 90
c = 161.699γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-28
    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, Source and taxonomy