1DP7

COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding.

Gajiwala, K.S.Chen, H.Cornille, F.Roques, B.P.Reith, W.Mach, B.Burley, S.K.

(2000) Nature 403: 916-921

  • DOI: 10.1038/35002634
  • Primary Citation of Related Structures:  
    1DP7

  • PubMed Abstract: 
  • Regulatory factor X (RFX) proteins are transcriptional activators that recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD) ...

    Regulatory factor X (RFX) proteins are transcriptional activators that recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD). DNA-binding defects in the protein RFX5 cause bare lymphocyte syndrome or major histocompatibility antigen class II deficiency. RFX1, -2 and -3 regulate expression of other medically important gene products (for example, interleukin-5 receptor alpha chain, IL-5R alpha). Fusions of the ligand-binding domain of the oestrogen receptor with the DBD of RFX4 occur in some human breast tumours. Here we present a 1.5 A-resolution structure of two copies of the DBD of human RFX1 (hRFX1) binding cooperatively to a symmetrical X-box. hRFX1 is an unusual member of the winged-helix subfamily of helix-turn-helix proteins because it uses a beta-hairpin (or wing) to recognize DNA instead of the recognition helix typical of helix-turn-helix proteins. A new model for interactions between linker histones and DNA is proposed.


    Related Citations: 
    • Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5
      Clark, K.L., Halay, E.D., Lai, E., Burley, S.K.
      (1993) Nature 364: 412
    • Crystal structure of globular domain of histone H5 and its implications for nucleosome binding
      Ramakrishnan, V., Finch, J., Graziano, V., Sweet, R.
      (1993) Nature 362: 219
    • A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity
      Emery, P., Strubin, M., Hofmann, K., Bucher, P., Mach, B., Reith, W.
      (1996) Mol Cell Biol 16: 4486
    • RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins
      Reith, W., Ucla, C., Barras, E., Gaud, A., Durand, B., Herrero-Sanchez, C., Kobr, M., Mach, B.
      (1994) Mol Cell Biol 14: 1230
    • DNA binding properties of a chemically synthesized DNA binding domain of hRFX1
      Cornille, F., Emery, P., Schuler, W., Lenoir, C., Mach, B., Roques, B.P., Reith, W.
      (1998) Nucleic Acids Res 26: 2143

    Organizational Affiliation

    Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II TRANSCRIPTION FACTOR HRFX1B [auth P]76N/AMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P22670 (Homo sapiens)
Explore P22670 
Go to UniProtKB:  P22670
PHAROS:  P22670
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')A [auth D]16N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PEG
    Query on PEG

    Download Ideal Coordinates CCD File 
    E [auth P]DI(HYDROXYETHYL)ETHER
    C4 H10 O3
    MTHSVFCYNBDYFN-UHFFFAOYSA-N
     Ligand Interaction
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    C [auth P], D [auth P]1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 Å
    • R-Value Free: 0.228 
    • R-Value Work: 0.192 
    • R-Value Observed: 0.192 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 72.843α = 90
    b = 42.752β = 109.21
    c = 52.277γ = 90
    Software Package:
    Software NamePurpose
    SOLVEphasing
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-03-06
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2021-02-03
      Changes: Database references, Derived calculations, Structure summary