2QFJ

Crystal Structure of First Two RRM Domains of FIR Bound to ssDNA from a Portion of FUSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition

Crichlow, G.V.Zhou, H.Hsiao, H.-H.Frederick, K.B.Debrosse, M.Yang, Y.Folta-Stogniew, E.J.Chung, H.-J.Fan, C.De La Cruz, E.M.Levens, D.Lolis, E.Braddock, D.

(2007) EMBO J. 27: 277-289

  • DOI: 10.1038/sj.emboj.7601936
  • Also Cited By: 5KWQ, 5KW6, 5KW1

  • PubMed Abstract: 
  • c-myc is essential for cell homeostasis and growth but lethal if improperly regulated. Transcription of this oncogene is governed by the counterbalancing forces of two proteins on TFIIH--the FUSE binding protein (FBP) and the FBP-interacting represso ...

    c-myc is essential for cell homeostasis and growth but lethal if improperly regulated. Transcription of this oncogene is governed by the counterbalancing forces of two proteins on TFIIH--the FUSE binding protein (FBP) and the FBP-interacting repressor (FIR). FBP and FIR recognize single-stranded DNA upstream of the P1 promoter, known as FUSE, and influence transcription by oppositely regulating TFIIH at the promoter site. Size exclusion chromatography coupled with light scattering reveals that an FIR dimer binds one molecule of single-stranded DNA. The crystal structure confirms that FIR binds FUSE as a dimer, and only the N-terminal RRM domain participates in nucleic acid recognition. Site-directed mutations of conserved residues in the first RRM domain reduce FIR's affinity for FUSE, while analogous mutations in the second RRM domain either destabilize the protein or have no effect on DNA binding. Oppositely oriented DNA on parallel binding sites of the FIR dimer results in spooling of a single strand of bound DNA, and suggests a mechanism for c-myc transcriptional control.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FBP-interacting repressor
A, B
216Homo sapiensMutation(s): 3 
Gene Names: PUF60 (FIR, ROBPI, SIAHBP1)
Find proteins for Q9UHX1 (Homo sapiens)
Go to Gene View: PUF60
Go to UniProtKB:  Q9UHX1
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DCP*DGP*DGP*DGP*DAP*DTP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DTP*DTP*DGP*DTP*DGP*DTP*DTP*DAP*DTP*DT)-3')C25N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 63.135α = 90.00
b = 63.135β = 90.00
c = 82.589γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SOLVEphasing
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description