1UN6

THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Zinc-Finger-RNA Complex Reveals Two Modes of Molecular Recognition

Lu, D.Searles, M.A.Klug, A.

(2003) Nature 426: 96

  • DOI: 10.1038/nature02088

  • PubMed Abstract: 
  • Zinc-finger proteins of the classical Cys2His2 type are the most frequently used class of transcription factor and account for about 3% of genes in the human genome. The zinc-finger motif was discovered during biochemical studies on the transcription ...

    Zinc-finger proteins of the classical Cys2His2 type are the most frequently used class of transcription factor and account for about 3% of genes in the human genome. The zinc-finger motif was discovered during biochemical studies on the transcription factor TFIIIA, which regulates the 5S ribosomal RNA genes of Xenopus laevis. Zinc-fingers mostly interact with DNA, but TFIIIA binds not only specifically to the promoter DNA, but also to 5S RNA itself. Increasing evidence indicates that zinc-fingers are more widely used to recognize RNA. There have been numerous structural studies on DNA binding, but none on RNA binding by zinc-finger proteins. Here we report the crystal structure of a three-finger complex with 61 bases of RNA, derived from the central regions of the complete nine-finger TFIIIA-5S RNA complex. The structure reveals two modes of zinc-finger binding, both of which differ from that in common use for DNA: first, the zinc-fingers interact with the backbone of a double helix; and second, the zinc-fingers specifically recognize individual bases positioned for access in otherwise intricately folded 'loop' regions of the RNA.


    Related Citations: 
    • The Role of the Central Zinc Fingers of Transcription Factor Iiia in Binding to 5S RNA
      Searles, M.A.,Lu, D.,Klug, A.
      (2000) J.Mol.Biol. 301: 47


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION FACTOR IIIA
B, C, D
87Xenopus laevisGene Names: gtf3a
Find proteins for P03001 (Xenopus laevis)
Go to UniProtKB:  P03001
Entity ID: 2
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAE,F61Xenopus laevis
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.598α = 90.00
b = 191.593β = 101.51
c = 79.770γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSphasing
CCP4phasing
SHARPphasing
SHELXphasing
CNSmodel building
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance