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PDBsum entry 2evz
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RNA binding protein
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PDB id
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2evz
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Contents |
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* Residue conservation analysis
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DOI no:
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EMBO J
25:150-162
(2006)
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PubMed id:
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Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling.
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F.Vitali,
A.Henning,
F.C.Oberstrass,
Y.Hargous,
S.D.Auweter,
M.Erat,
F.H.Allain.
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ABSTRACT
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The polypyrimidine tract binding protein (PTB) is a 58 kDa protein involved in
many aspects of RNA metabolism. In this study, we focused our attention on the
structure of the two C-terminal RNA recognition motifs (RRM3 and RRM4) of PTB.
In a previous study, it was found that the two RRMs are independent in the free
state. We recently determined the structure of the same fragment in complex with
RNA and found that the two RRMs interact extensively. This difference made us
re-evaluate in detail the free protein structure and in particular the
interdomain interface. We used a combination of NMR spectroscopy and segmental
isotopic labeling to unambiguously study and characterize the interdomain
interactions. An improved segmental isotopic labeling protocol was used,
enabling us to unambiguously identify 130 interdomain NOEs between the two RRMs
and to calculate a very precise structure. The structure reveals a large
interdomain interface, resulting in a very unusual positioning of the two RRM
domains relative to one another.
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Selected figure(s)
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Figure 1.
Figure 1 Protein constructs used in this study. Protein domains
are represented by colored boxes: orange for the NLS sequence;
white for linker regions; pink for PTB RRM1; violet for PTB
RRM2; red for PTB RRM3 domain; yellow for PTB RRM4; gray for 6
 His
tag; blue for CBD; light blue for the Mxe GyrA intein; and green
for the Ssp DnaB intein.
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Figure 6.
Figure 6 Close-up view of the interdomain interface in PTB RRM34
and hnRNPA1 RRM12. (A) Stereo view of the interaction between
helix 2 of RRM4 and helix 1 of RRM3. Side chains for RRM3 and
RRM4 and the interdomain linker are represented by sticks and
dotted surfaces colored in blue, green and red, respectively.
(B) Stereo view of the interaction between helix 2 of RRM3 with
the interdomain linker and F526 from RRM4. (C) Stereo view of
the interdomain interface found in the structure of hnRNPA1
RRM12 (Shamoo et al, 1997).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2006,
25,
150-162)
copyright 2006.
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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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A.Cléry,
S.Jayne,
N.Benderska,
C.Dominguez,
S.Stamm,
and
F.H.Allain
(2011).
Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1.
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Nat Struct Mol Biol,
18,
443-450.
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PDB code:
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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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C.M.Maynard,
and
K.B.Hall
(2010).
Interactions between PTB RRMs induce slow motions and increase RNA binding affinity.
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J Mol Biol,
397,
260-277.
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G.Volkmann,
and
H.Iwaï
(2010).
Protein trans-splicing and its use in structural biology: opportunities and limitations.
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Mol Biosyst,
6,
2110-2121.
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I.Díaz-Moreno,
D.Hollingworth,
G.Kelly,
S.Martin,
M.García-Mayoral,
P.Briata,
R.Gherzi,
and
A.Ramos
(2010).
Orientation of the central domains of KSRP and its implications for the interaction with the RNA targets.
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Nucleic Acids Res,
38,
5193-5205.
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L.Skrisovska,
M.Schubert,
and
F.H.Allain
(2010).
Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins.
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J Biomol NMR,
46,
51-65.
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M.Vila-Perelló,
and
T.W.Muir
(2010).
Biological applications of protein splicing.
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Cell,
143,
191-200.
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R.Lamichhane,
G.M.Daubner,
J.Thomas-Crusells,
S.D.Auweter,
C.Manatschal,
K.S.Austin,
O.Valniuk,
F.H.Allain,
and
D.Rueda
(2010).
RNA looping by PTB: Evidence using FRET and NMR spectroscopy for a role in splicing repression.
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Proc Natl Acad Sci U S A,
107,
4105-4110.
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S.P.Han,
Y.H.Tang,
and
R.Smith
(2010).
Functional diversity of the hnRNPs: past, present and perspectives.
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Biochem J,
430,
379-392.
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C.Clerte,
and
K.B.Hall
(2009).
The domains of polypyrimidine tract binding protein have distinct RNA structural preferences.
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Biochemistry,
48,
2063-2074.
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D.Liu,
R.Xu,
and
D.Cowburn
(2009).
Segmental isotopic labeling of proteins for nuclear magnetic resonance.
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Methods Enzymol,
462,
151-175.
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A.Cléry,
M.Blatter,
and
F.H.Allain
(2008).
RNA recognition motifs: boring? Not quite.
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Curr Opin Struct Biol,
18,
290-298.
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G.V.Crichlow,
H.Zhou,
H.H.Hsiao,
K.B.Frederick,
M.Debrosse,
Y.Yang,
E.J.Folta-Stogniew,
H.J.Chung,
C.Fan,
E.M.De la Cruz,
D.Levens,
E.Lolis,
and
D.Braddock
(2008).
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition.
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EMBO J,
27,
277-289.
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PDB code:
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M.S.Jurica
(2008).
Detailed close-ups and the big picture of spliceosomes.
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Curr Opin Struct Biol,
18,
315-320.
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W.Zhao,
Y.Zhang,
C.Cui,
Q.Li,
and
J.Wang
(2008).
An efficient on-column expressed protein ligation strategy: application to segmental triple labeling of human apolipoprotein E3.
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Protein Sci,
17,
736-747.
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E.Bae,
N.J.Reiter,
C.A.Bingman,
S.S.Kwan,
D.Lee,
G.N.Phillips,
S.E.Butcher,
and
D.A.Brow
(2007).
Structure and interactions of the first three RNA recognition motifs of splicing factor prp24.
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J Mol Biol,
367,
1447-1458.
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PDB codes:
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C.Dominguez,
and
F.H.Allain
(2006).
NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition.
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Nucleic Acids Res,
34,
3634-3645.
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PDB codes:
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J.Saulière,
A.Sureau,
A.Expert-Bezançon,
and
J.Marie
(2006).
The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit.
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Mol Cell Biol,
26,
8755-8769.
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M.V.Petoukhov,
T.P.Monie,
F.H.Allain,
S.Matthews,
S.Curry,
and
D.I.Svergun
(2006).
Conformation of polypyrimidine tract binding protein in solution.
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Structure,
14,
1021-1027.
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S.D.Auweter,
F.C.Oberstrass,
and
F.H.Allain
(2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
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Nucleic Acids Res,
34,
4943-4959.
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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
