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PDBsum entry 1hd1
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RNA binding protein
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PDB id
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1hd1
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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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Structure and interactions with RNA of the n-Terminal uuag-Specific RNA-Binding domain of hnrnp d0.
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Authors
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T.Nagata,
Y.Kurihara,
G.Matsuda,
J.Saeki,
T.Kohno,
Y.Yanagida,
F.Ishikawa,
S.Uesugi,
M.Katahira.
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Ref.
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J Mol Biol, 1999,
287,
221-237.
[DOI no: ]
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PubMed id
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Abstract
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Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 has two ribonucleoprotein
(RNP)-type RNA-binding domains (RBDs), each of which can bind solely to the UUAG
sequence specifically. The structure of the N-terminal RBD (RBD1) determined by
NMR is presented here. It folds into a compact alphabeta structure comprising a
four-stranded antiparallel beta-sheet packed against two alpha-helices, which is
characteristic of the RNP-type RBDs. Special structural features of RBD1 include
N-capping boxes for both alpha-helices, a beta-bulge in the second beta-strand,
and an additional short antiparallel beta-sheet coupled with a beta-turn-like
structure in a loop. Two hydrogen bonds which restrict the positions of loops
were identified. Backbone resonance assignments for RBD1 complexed with
r(UUAGGG) revealed that the overall folding is maintained in the complex. The
candidate residues involved in the interactions with RNA were identified by
chemical shift perturbation analysis. They are located in the central and
peripheral regions of the RNA-binding surface composed of the four-stranded
beta-sheet, loops, and the C-terminal region. It is suggested that non-specific
interactions with RNA are performed by the residues in the central region of the
RNA-binding surface, while specific interactions are performed by those in the
peripheral regions. It was also found that RBD1 has the ability to inhibit the
formation of the quadruplex structure.
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Figure 2.
Figure 2. The four-stranded antiparallel β-sheet of p112.
Interstrand NOEs are indicated by double-headed arrows. Slowly
exchanging amide protons are indicated by bold Hs. Hydrogen
bonds consistent with the NOEs and exchange data are indicated
by broken lines. Circles for C^α indicate that the side-chains
of these residues are presumed to be exposed to the solvent.
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Figure 3.
Figure 3. The structure of the 29–103 region of p112. (a)
Superposition of the main-chains of 20 refined structures for
the residues 29–103. N and C indicate K29 and A103,
respectively, and loop 3 is labeled. (b) Schematic drawing of
the restrained energy minimized mean structure derived from the
20 refined structures for 29–103, as viewed from the same
direction as in (a). (c) Hydrophobic core. Overlaying of the 20
structures of the side-chains for residues involved in the
hydrophobic core is shown on the main-chain of the restrained
energy minimized mean structure. The α-helices and β-strands
are colored in red and blue, respectively. (d) Hydrophobic patch
exposed to the solvent. The same overlaying as in (c) is shown
for F31, F71 and F73, being rotated by ca. 90 ° from (c).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
287,
221-237)
copyright 1999.
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