1DP7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 do ...

    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: 
    • 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
    • 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
    • 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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II TRANSCRIPTION FACTOR HRFX1
P
76Homo sapiensGene Names: RFX1
Find proteins for P22670 (Homo sapiens)
Go to Gene View: RFX1
Go to UniProtKB:  P22670
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')D16N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
P
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
P
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
D
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.843α = 90.00
b = 42.752β = 109.21
c = 52.277γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance