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PDBsum entry 1fje
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Structural protein/RNA
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PDB id
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1fje
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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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Molecular basis of sequence-Specific recognition of pre-Ribosomal RNA by nucleolin.
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Authors
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F.H.Allain,
P.Bouvet,
T.Dieckmann,
J.Feigon.
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Ref.
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EMBO J, 2000,
19,
6870-6881.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the 28 kDa complex of the first two RNA binding domains (RBDs)
of nucleolin (RBD12) with an RNA stem-loop that includes the nucleolin
recognition element UCCCGA in the loop was determined by NMR spectroscopy. The
structure of nucleolin RBD12 with the nucleolin recognition element (NRE)
reveals that the two RBDs bind on opposite sides of the RNA loop, forming a
molecular clamp that brings the 5' and 3' ends of the recognition sequence close
together and stabilizing the stem-loop. The specific interactions observed in
the structure explain the sequence specificity for the NRE sequence. Binding
studies of mutant proteins and analysis of conserved residues support the
proposed interactions. The mode of interaction of the protein with the RNA and
the location of the putative NRE sites suggest that nucleolin may function as an
RNA chaperone to prevent improper folding of the nascent pre-rRNA.
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Figure 3.
Figure 3 Overall description of the complex. The lowest energy
structure is shown. (A) Stick (RNA) and ribbon (protein)
representation of the complex showing how the RNA loop is
'sandwiched' between the two RBDs. RBD1 is located in the major
groove side of the RNA and contacts C12, G13 and the loop E
motif. RBD2 is located on the minor groove side and contacts U9
and C10. The linker is mostly located in the minor groove side
on the RNA. The amino acid side chains from RBD1 V27, K31 (  -helix
1) and T52, R54 (  2–
3
loop), which contact the stem, as well as the inserting residues
F56 and K94, are shown in blue. (B) Surface representation of
the RNA and protein complex. The view is the same as in (A). (C)
View of the complex showing that the two RBDs interact via two
salt bridges (K89–E125 and K55–D132). Asp and Glu are shown
in red and Lys and Arg in blue. The major groove face of the
binding site is shown. (D) GRASP (Nicholls et al., 1991)
representation of the complex with positively charged residues
in blue and negatively charged residues in red. The color scheme
is the same as Figure 2, except for the GRASP representation.
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Figure 8.
Figure 8 Proposed model of the RNA chaperone activity of
nucleolin for proper folding of the 5' ETS region between
nucleotides 1671 and 3549 of human 47S pre-rRNA. A schematic
representation of the predicted secondary structure of this
region in the mature pre-rRNA based on phylogeny (Renalier et
al., 1989) and electron microscopy (Wellauer et al., 1974;
Schibler et al., 1975) studies is shown on the right. The
putative NRE binding sites in this sequence are indicated by
black rectangles. They are all found in double-stranded regions
of the mature pre-rRNA, so nucleolin (indicated by the black
oval ring) is not expected to be bound. On the left side of the
figure are shown schematically two alternate structures that the
RNA can adopt with (top) or without (bottom) nucleolin. Without
nucleolin, the RNA can be kinetically trapped in alternative
stable structures, which have to unfold to form the mature
pre-rRNA, with the result that formation of the mature pre-rRNA
will be slow. The bound nucleolin promotes and/or stabilizes
stem–loops at the NRE consensus sites, preventing the
formation of alternative stable helices, and then dissociates to
allow the final structure to form.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2000,
19,
6870-6881)
copyright 2000.
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Secondary reference #1
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Title
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Solution structure of the two n-Terminal RNA-Binding domains of nucleolin and nmr study of the interaction with its RNA target.
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Authors
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F.H.Allain,
D.E.Gilbert,
P.Bouvet,
J.Feigon.
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Ref.
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J Mol Biol, 2000,
303,
227-241.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. (a) Schematic diagram of the domain structure of
nucleolin. (b) Consensus RNA secondary structure and loop
sequence found for nucleolin binding, the nucleolin recognition
element (NRE) [Ghisolfi-Nieto et al 1996]. (c) Amino acid
sequence of the protein constructs of RBD1, RBD2 and RBD12 from
hamster nucleolin. The numbering in each RBD corresponds to the
position in the RBD12 protein. Amino acid residues of RBD1, RBD2
and the linker are colored in black, red and green,
respectively. Secondary structure elements are indicated below
the sequence.
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Figure 3.
Figure 3. Stereoviews of the family of lowest energy
structures of (a) RBD1 and (b) RBD2. The 34 lowest energy
structures of RBD1 are shown superimposed on the backbone heavy
atoms of residue 14 to 87. The 33 lowest energy structures of
RBD2 are superimposed on the backbone heavy atoms of residue 93
to 171. The location of a-helix 1 (cyan), a-helix 2 (red) and
the first and last residues are indicated. The b2-b3 loop is
colored orange and the N-terminal helix on RBD2 is green. (c)
Ribbon representation of RBD12. Since the linker region (green)
is flexible and no NOEs are observed between the two RBDs, the
orientation of the two RBDs relative to one another is not
defined in solution. The structure shown has the two RBDs
oriented in such a way that their b-strands can interact with
the RNA. Side-chains of F17, Y58, L103, and Y140 shown on the
structure have intermolecular NOEs to the RNA loop nucleotides
(Figure 7).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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