1UN6

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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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
  • Primary Citation of Related Structures:  
    1UN6

  • 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 factor TFIIIA, which regulates the 5S ribosomal RNA genes of Xenopus laevis ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION FACTOR IIIAA [auth B],
B [auth C],
C [auth D]		87Xenopus laevisMutation(s): 0 
Gene Names: gtf3a
UniProt
Find proteins for P03001 (Xenopus laevis)
Explore P03001 
Go to UniProtKB:  P03001
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03001
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAD [auth E],
E [auth F]		61Xenopus laevis
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
F [auth B],
G [auth B],
H [auth B],
L [auth C],
M [auth C],
F [auth B],
G [auth B],
H [auth B],
L [auth C],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
K [auth B],
O [auth C],
P [auth C],
I [auth B],
J [auth B],
K [auth B],
O [auth C],
P [auth C],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth F],
X [auth F],
Y [auth F],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.598α = 90
b = 191.593β = 101.51
c = 79.77γ = 90
Software Package:
Software NamePurpose
CNSmodel building
SCALAdata scaling
CCP4phasing
SHELXphasing
SHARPphasing
CNSphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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