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PDBsum entry 1un6
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RNA-binding protein/RNA
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PDB id
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1un6
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a zinc-Finger-Rna complex reveals two modes of molecular recognition.
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Authors
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D.Lu,
M.A.Searles,
A.Klug.
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Ref.
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Nature, 2003,
426,
96.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 3.
Figure 3: Recognition of loop E by finger 4. a, Structure of
loop E. The chains are coloured as in Fig. 2a. Hydrogen bonds
are shown in red, and base stacking in green. Stacking
interactions are assigned according to the degree of overlap and
have separation distances shorter than 3.8 Å. b, Interaction of
loop E with the N terminus of the helix of finger 4. Colours are
the same as in a, with peptide side chains in yellow. The
hydrogen-bond interactions between protein and RNA are listed in
Fig. 2c. The bulged base 75G is gripped by hydrogen bonds from
Asp 120 and His 119, and its ribose by a hydrogen bond from Lys
118.
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Figure 4.
Figure 4: Recognition of loop A by finger 6. a, Structure of
loop A. Three colours are used to indicate the three-way
junction, blue and purple as in Figs 2 and 3, but with
nucleotides 64-68 in orange. b, Interaction of loop A with the N
terminus of the helix of finger 6. Peptide side chains are shown
in yellow. The ring of Trp 177 docks on the face of base 11A,
and the two flanking residues, Thr 176 and Thr 178, make
hydrogen bonds to base 10C. Trp 177 also makes a hydrogen bond
to the ribose of 13A.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2003,
426,
96-0)
copyright 2003.
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Secondary reference #1
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Title
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The role of the central zinc fingers of transcription factor iiia in binding to 5 s RNA.
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Authors
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M.A.Searles,
D.Lu,
A.Klug.
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Ref.
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J Mol Biol, 2000,
301,
47-60.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Secondary structure of Xenopus laevis oocyte 5 S
RNA.
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Figure 5.
Figure 5. Mobility shift gels of the interaction of
TFIIIA(4-6) and TFIIIA(4-7) with full-length 5 S RNA and
truncated mutants.  triange,
filled , total RNA concentrations (nM).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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