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 1.5 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: https://doi.org/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). 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.


  • 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)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence 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
GTEx:  ENSG00000132005 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22670
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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  • Reference Sequence
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
  • Version 1.4: 2021-11-03
    Changes: Database references
  • Version 1.5: 2024-02-07
    Changes: Data collection