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 
  • R-Value Observed: 0.245 

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
  • Primary Citation of Related Structures:  
    1H88, 1H89, 1H8A

  • 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 ...

    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
      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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAAT/ENHANCER BINDING PROTEIN BETAA, B78Homo sapiensMutation(s): 0 
Gene Names: CEBPB, TCF5, PP9092
UniProt & NIH Common Fund Data Resources
Find proteins for P17676 (Homo sapiens)
Explore P17676 
Go to UniProtKB:  P17676
PHAROS:  P17676
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17676
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MYB TRANSFORMING PROTEINC128Avian myeloblastosis virusMutation(s): 0 
Gene Names: V-MYB
UniProt
Find proteins for P01104 (Avian myeloblastosis virus)
Explore P01104 
Go to UniProtKB:  P01104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01104
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1H8A Kd: 25.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.86α = 90
b = 166.7β = 90
c = 39.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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