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* Residue conservation analysis
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PDB id:
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RNA-binding protein/RNA
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Title:
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The crystal structure of a zinc finger - RNA complex reveals two modes of molecular recognition
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Structure:
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Transcription factor iiia. Chain: b, c, d. Fragment: fingers 4,5 and 6, residues 127 - 212 under swissprot numbering for somatic tfiiia. Synonym: tfiiia, factor a, s-tfiiia/o-tfiiia. Engineered: yes. 5s ribosomal RNA. Chain: e, f. Fragment: central region, nucleotides 4 - 15,64 -82,94-115, plus two
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Source:
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Xenopus laevis. African clawed frog. Organism_taxid: 8355. Organ: ovary. Cell: oocyte. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: in vitro transcription to produce the RNA
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Biol. unit:
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Dimer (from PDB file)
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Resolution:
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3.10Å
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R-factor:
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0.216
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R-free:
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0.259
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Authors:
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D.Lu,M.A.Searles,A.Klug
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Key ref:
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D.Lu
et al.
(2003).
Crystal structure of a zinc-finger-RNA complex reveals two modes of molecular recognition.
Nature,
426,
96.
PubMed id:
DOI:
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Date:
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04-Sep-03
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Release date:
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20-Nov-03
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PROCHECK
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Headers
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References
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DOI no:
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Nature
426:96
(2003)
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PubMed id:
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Crystal structure of a zinc-finger-RNA complex reveals two modes of molecular recognition.
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D.Lu,
M.A.Searles,
A.Klug.
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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Dominguez,
M.Schubert,
O.Duss,
S.Ravindranathan,
and
F.H.Allain
(2011).
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
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Prog Nucl Magn Reson Spectrosc,
58,
1.
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J.P.Mackay,
J.Font,
and
D.J.Segal
(2011).
The prospects for designer single-stranded RNA-binding proteins.
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Nat Struct Mol Biol,
18,
256-261.
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M.Doetsch,
R.Schroeder,
and
B.Fürtig
(2011).
Transient RNA-protein interactions in RNA folding.
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FEBS J,
278,
1634-1642.
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|
|
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|
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S.M.Quintal,
Q.A.dePaula,
and
N.P.Farrell
(2011).
Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences.
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Metallomics,
3,
121-139.
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X.J.Lu,
W.K.Olson,
and
H.J.Bussemaker
(2010).
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.
|
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Nucleic Acids Res,
38,
4868-4876.
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|
|
|
|
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D.A.Pomeranz Krummel,
C.Oubridge,
A.K.Leung,
J.Li,
and
K.Nagai
(2009).
Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
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Nature,
458,
475-480.
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PDB code:
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D.F.Estrada,
D.M.Boudreaux,
D.Zhong,
S.C.St Jeor,
and
R.N.De Guzman
(2009).
The Hantavirus Glycoprotein G1 Tail Contains Dual CCHC-type Classical Zinc Fingers.
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J Biol Chem,
284,
8654-8660.
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PDB code:
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F.E.Loughlin,
R.E.Mansfield,
P.M.Vaz,
A.P.McGrath,
S.Setiyaputra,
R.Gamsjaeger,
E.S.Chen,
B.J.Morris,
J.M.Guss,
and
J.P.Mackay
(2009).
The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences.
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Proc Natl Acad Sci U S A,
106,
5581-5586.
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PDB code:
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H.Tidow,
A.Andreeva,
T.J.Rutherford,
and
A.R.Fersht
(2009).
Solution structure of the U11-48K CHHC zinc-finger domain that specifically binds the 5' splice site of U12-type introns.
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Structure,
17,
294-302.
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PDB codes:
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S.H.Mishra,
A.M.Spring,
and
M.W.Germann
(2009).
Thermodynamic profiling of HIV RREIIB RNA-zinc finger interactions.
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J Mol Biol,
393,
369-382.
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|
|
|
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|
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A.Smirnov,
I.Tarassov,
A.M.Mager-Heckel,
M.Letzelter,
R.P.Martin,
I.A.Krasheninnikov,
and
N.Entelis
(2008).
Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria.
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RNA,
14,
749-759.
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K.J.Brayer,
and
D.J.Segal
(2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
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Cell Biochem Biophys,
50,
111-131.
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K.J.Brayer,
S.Kulshreshtha,
and
D.J.Segal
(2008).
The protein-binding potential of C2H2 zinc finger domains.
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Cell Biochem Biophys,
51,
9.
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M.Teplova,
and
D.J.Patel
(2008).
Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1.
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Nat Struct Mol Biol,
15,
1343-1351.
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PDB codes:
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X.Guo,
N.L.Ernst,
and
K.D.Stuart
(2008).
The KREPA3 zinc finger motifs and OB-fold domain are essential for RNA editing and survival of Trypanosoma brucei.
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Mol Cell Biol,
28,
6939-6953.
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Y.Chen,
J.Mandic,
and
G.Varani
(2008).
Cell-free selection of RNA-binding proteins using in vitro compartmentalization.
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Nucleic Acids Res,
36,
e128.
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B.M.Lunde,
C.Moore,
and
G.Varani
(2007).
RNA-binding proteins: modular design for efficient function.
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Nat Rev Mol Cell Biol,
8,
479-490.
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D.Lu,
and
A.Klug
(2007).
Invariance of the zinc finger module: a comparison of the free structure with those in nucleic-acid complexes.
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Proteins,
67,
508-512.
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PDB code:
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F.He,
T.Umehara,
K.Tsuda,
M.Inoue,
T.Kigawa,
T.Matsuda,
T.Yabuki,
M.Aoki,
E.Seki,
T.Terada,
M.Shirouzu,
A.Tanaka,
S.Sugano,
Y.Muto,
and
S.Yokoyama
(2007).
Solution structure of the zinc finger HIT domain in protein FON.
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Protein Sci,
16,
1577-1587.
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PDB code:
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M.A.Tijms,
D.D.Nedialkova,
J.C.Zevenhoven-Dobbe,
A.E.Gorbalenya,
and
E.J.Snijder
(2007).
Arterivirus subgenomic mRNA synthesis and virion biogenesis depend on the multifunctional nsp1 autoprotease.
|
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J Virol,
81,
10496-10505.
|
|
|
|
|
|
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Y.Yuan,
S.A.Compton,
K.Sobczak,
M.G.Stenberg,
C.A.Thornton,
J.D.Griffith,
and
M.S.Swanson
(2007).
Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs.
|
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Nucleic Acids Res,
35,
5474-5486.
|
|
|
|
|
|
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Z.R.Belak,
and
N.Ovsenek
(2007).
Assembly of the Yin Yang 1 transcription factor into messenger ribonucleoprotein particles requires direct RNA binding activity.
|
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J Biol Chem,
282,
37913-37920.
|
|
|
|
|
|
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A.V.Giesecke,
R.Fang,
and
J.K.Joung
(2006).
Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers.
|
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Mol Syst Biol,
2,
2006.2011.
|
|
|
|
|
|
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C.Fan,
J.Yan,
Y.Qian,
X.Wo,
and
L.Gao
(2006).
Regulation of lipoprotein lipase expression by effect of hawthorn flavonoids on peroxisome proliferator response element pathway.
|
| |
J Pharmacol Sci,
100,
51-58.
|
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|
|
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|
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F.C.Oberstrass,
A.Lee,
R.Stefl,
M.Janis,
G.Chanfreau,
and
F.H.Allain
(2006).
Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.
|
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Nat Struct Mol Biol,
13,
160-167.
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PDB codes:
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G.J.Kornhaber,
D.Snyder,
H.N.Moseley,
and
G.T.Montelione
(2006).
Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.
|
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J Biomol NMR,
34,
259-269.
|
|
|
|
|
|
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M.Howard-Ashby,
S.C.Materna,
C.T.Brown,
Q.Tu,
P.Oliveri,
R.A.Cameron,
and
E.H.Davidson
(2006).
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution.
|
| |
Dev Biol,
300,
27-34.
|
|
|
|
|
|
|
S.H.Mishra,
C.M.Shelley,
D.J.Barrow,
M.K.Darby,
and
M.W.Germann
(2006).
Solution structures and characterization of human immunodeficiency virus Rev responsive element IIB RNA targeting zinc finger proteins.
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Biopolymers,
83,
352-364.
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PDB codes:
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S.Ladame,
J.A.Schouten,
J.Roldan,
J.E.Redman,
S.Neidle,
and
S.Balasubramanian
(2006).
Exploring the recognition of quadruplex DNA by an engineered Cys2-His2 zinc finger protein.
|
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Biochemistry,
45,
1393-1399.
|
|
|
|
|
|
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A.Lingel,
B.Simon,
E.Izaurralde,
and
M.Sattler
(2005).
The structure of the flock house virus B2 protein, a viral suppressor of RNA interference, shows a novel mode of double-stranded RNA recognition.
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EMBO Rep,
6,
1149-1155.
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PDB code:
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A.Longo,
C.W.Leonard,
G.S.Bassi,
D.Berndt,
J.M.Krahn,
T.M.Hall,
and
K.M.Weeks
(2005).
Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.
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Nat Struct Mol Biol,
12,
779-787.
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PDB code:
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A.M.Bonvin,
R.Boelens,
and
R.Kaptein
(2005).
NMR analysis of protein interactions.
|
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Curr Opin Chem Biol,
9,
501-508.
|
|
|
|
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|
K.L.Brady,
S.N.Ponnampalam,
M.J.Bumbulis,
and
D.R.Setzer
(2005).
Mutations in TFIIIA that increase stability of the TFIIIA-5 S rRNA gene complex: unusual effects on the kinetics of complex assembly and dissociation.
|
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J Biol Chem,
280,
26743-26750.
|
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|
|
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|
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R.Stefl,
L.Skrisovska,
and
F.H.Allain
(2005).
RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle.
|
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EMBO Rep,
6,
33-38.
|
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|
|
|
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T.M.Hall
(2005).
Multiple modes of RNA recognition by zinc finger proteins.
|
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Curr Opin Struct Biol,
15,
367-373.
|
|
|
|
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Y.Chen,
and
G.Varani
(2005).
Protein families and RNA recognition.
|
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FEBS J,
272,
2088-2097.
|
|
|
|
|
|
|
B.Lehner,
and
A.G.Fraser
(2004).
Protein domains enriched in mammalian tissue-specific or widely expressed genes.
|
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Trends Genet,
20,
468-472.
|
|
|
|
|
|
|
H.Zhang,
A.Christoforou,
L.Aravind,
S.W.Emmons,
S.van den Heuvel,
and
D.A.Haber
(2004).
The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein.
|
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Mol Cell,
14,
841-847.
|
|
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|
|
|
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L.Jeffery,
and
S.Nakielny
(2004).
Components of the DNA methylation system of chromatin control are RNA-binding proteins.
|
| |
J Biol Chem,
279,
49479-49487.
|
|
|
|
|
|
|
R.J.Simpson,
S.H.Yi Lee,
N.Bartle,
E.Y.Sum,
J.E.Visvader,
J.M.Matthews,
J.P.Mackay,
and
M.Crossley
(2004).
A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.
|
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J Biol Chem,
279,
39789-39797.
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PDB code:
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J.M.Berg
(2003).
Fingering nucleic acids: the RNA did it.
|
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Nat Struct Biol,
10,
986-987.
|
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
