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PDBsum entry 2ozb
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RNA binding protein/RNA
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PDB id
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2ozb
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References listed in PDB file
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Key reference
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Title
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Binding of the human prp31 nop domain to a composite RNA-Protein platform in u4 snrnp.
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Authors
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S.Liu,
P.Li,
O.Dybkov,
S.Nottrott,
K.Hartmuth,
R.Lührmann,
T.Carlomagno,
M.C.Wahl.
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Ref.
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Science, 2007,
316,
115-120.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and
Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles.
hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac
small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small
nucleolar RNA complexes. We present structural and biochemical analyses of
hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31
maintains high RNP binding selectivity despite relaxed RNA sequence
requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and
protein binding surfaces. Yeast two-hybrid analyses suggest a link between
retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks
U4/U6-U5 tri-snRNP formation.
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Figure 1.
Fig. 1. (A) Schematics of the 5'-SLs of U4 snRNA (left), U4atac
snRNA (middle), and the K-turn region of box C/D snoRNAs
(right). N indicates any nucleotide; R, purine. Binding of 15.5K
and the secondary binding proteins is indicated. Stem II of the
K turn in the box C/D snoRNAs is longer by one base pair (20),
and a single additional base pair in stem II is known to
interfere with hPrp31 binding (21). Box C/D snoRNPs act as
sequence-specific 2'-O methyltransferases, which
posttranscriptionally modify several functional RNAs. (B)(Left)
^1H-^15N heteronuclear singlequantum coherence spectra of 15.5K
in the binary 15.5K–U4 5'-SL complex (black) and in the
ternary complex containing full-length hPrp31 (red). Assignments
of selected resonances are indicated. ppm, parts per million.
(Middle) Mapping of NMR chemical shift changes elicited by the
addition of hPrp31 on the structure of the 15.5K-RNA complex
[coordinates from (12); PDB ID 1E7K]. Dashed line is the
disordered pentaloop of the RNA; 15.5K, light gray; and RNA,
dark gray. All structure figures were prepared with PyMOL (34).
(Right) Mapping of saturation transfer from hPrp31 to RNA-bound
15.5K, indicating residues of 15.5K that are directly contacted
by hPrp31. Apparent contacts to the central ß sheet of
15.5K arise from spin diffusion. Degrees of chemical shift
changes and saturation transfer are color-coded: red, strong;
orange, intermediate; and yellow, weak. A similar picture is
obtained when mapping the contacts of hPrp31^78-333 on 15.5K in
the framework of the 15.5K–U4 5'-SL complex (SOM text),
confirming that the hPrp31^78-333 fragment interacts with 15.5K
in the same way as the full-length protein.
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Figure 2.
Fig. 2. (A) Overview of the hPrp31^78-333–15.5K–U4 5'-SL
complex (left). hPrp31^78-333, blue; 15.5K, red; RNA, gold. RNA
elements not seen in the binary 15.5K–22-mer RNA complex with
a shorter stem I [right (12); PDB ID 1E7K] are in green.
Positions A194 and A216, at which missense mutations have been
linked to the RP11 form of retinitis pigmentosa, are shown as
space-filling models and colored cyan. Dashed line in
hPrp31^78-333, disordered loop. Dashed line in the binary
complex, unstructured pentaloop. Although induced-fit
interactions are the hallmark of most RNA-protein complexes
(32), the structuring of the RNA pentaloop upon hPrp31^78-333
binding observed here is particularly pronounced. The crystal
structure contains two crystallographically independent ternary
complexes per asymmetric unit that are largely identical (table
S2). (B) Close-up views of the complex from the back (left) and
from the bottom (right). Main contact regions between
hPrp31^78-333 and 15.5K and between hPrp31^78-333 and the RNA
are indicated by connecting lines and are labeled by letters and
numbers, respectively. Regions of the RNA are color-coded:
distal portion of stem I, gray; K-turn region, gold; distal
portion of stem II, brown; and pentaloop, beige. The bulged-out
U31 denotes the tip of the K turn and is shown in sticks.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2007,
316,
115-120)
copyright 2007.
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