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PDBsum entry 462d
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References listed in PDB file
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Key reference
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Title
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The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.
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Authors
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E.Ennifar,
M.Yusupov,
P.Walter,
R.Marquet,
B.Ehresmann,
C.Ehresmann,
P.Dumas.
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Ref.
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Structure, 1999,
7,
1439-1449.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: An important step in retroviral replication is dimerization of the
genomic RNA prior to encapsidation. Dimerization is initiated by the formation
of a transient 'kissing-loop complex' that is thought to be subsequently matured
into an extended duplex by the nucleocapsid protein (NCp). Although chemical
probing and nuclear magnetic resonance spectroscopy have provided insight into
the structure of the kissing-loop structure, no structural information
concerning the extended-duplex state is available so far. RESULTS: The structure
of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A
resolution in two different space groups. It reveals a 22 base pair extended
duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to
a bulged-out adenine. The structure shows significant asymmetry in deep groove
width and G-A base-pair conformations. A network of eight magnesium cations was
clearly identified, one being unusually chelated by the 3' phosphate of each
bulge across an extremely narrowed deep major groove. CONCLUSIONS: These crystal
structures represent the putative matured form of the initial kissing-loop
complex. They show the ability of this self-complementary RNA hairpin loop to
acquire a more stable extended duplex structure. Both bulged adenines form a
striking 'base grip' that could be a recognition signal, either in cis for
another viral RNA sequence, or in trans for a protein, possibly the NCp.
Magnesium binding might be important to promote and stabilize the observed
extrahelical conformation of these bulges.
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Figure 6.
Figure 6. Stereoviews showing the closing of the deep
groove in the vicinity of the bulges and three magnesium cations
with direct coordination to phosphates and N7 atoms (trigonal
form). (a) Axial coordination of Mg d by the phosphates of G9a
and G9b. Mg g and g' are each localized in a pocket formed by
the phosphate of A8 and the N7 of G9 of strands b and a,
respectively. The ribose of A8a adopts the C3' endo/O4' endo
conformation and its base is in the syn conformation, whereas
the ribose of A8b is shown here in one of the two conformations
(C2' endo). The line of sight is along the noncrystallographic
dyad axis. (b) Representative (2F[obs]-F[calc]) electron-density
map (light blue), superimposed with the (FMn[obs]-FMg[calc])
Fourier difference map (orange), contoured at 4s around site d
and at 6s around sites g and g' (see the Materials and methods
section).
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1999,
7,
1439-1449)
copyright 1999.
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Headers
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