1H88

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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

  • 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 ...

    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 --: --

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CCAAT/ENHANCER BINDING PROTEIN BETAA, B78Homo sapiensMutation(s): 0 
Gene Names: CEBPBTCF5PP9092
Find proteins for P17676 (Homo sapiens)
Explore P17676 
Go to UniProtKB:  P17676
NIH Common Fund Data Resources
PHAROS  P17676
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MYB PROTO-ONCOGENE PROTEINC159Mus musculusMutation(s): 2 
Gene Names: Myb
Find proteins for P06876 (Mus musculus)
Explore P06876 
Go to UniProtKB:  P06876
NIH Common Fund Data Resources
IMPC  MGI:97249
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  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
Find similar nucleic acids by: 
(by identity cutoff)  |  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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH4
Query on NH4

Download CCD File 
C
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd :  35.29999923706055   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.735α = 90
b = 156.966β = 100.16
c = 55.868γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-28
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other, Source and taxonomy