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PDBsum entry 1duq
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PDB id:
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RNA
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Title:
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Crystal structure of the rev binding element of HIV-1
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Structure:
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The rev binding element. Chain: a, c, e, g. Fragment: short chain. Engineered: yes. The rev binding element. Chain: b, d, f, h. Fragment: long chain. Engineered: yes
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Source:
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Synthetic: yes. Other_details: sequence from HIV-1. Synthesized by oligos, etc.. Synthetic: yes
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Biol. unit:
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Dimer (from
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Resolution:
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2.10Å
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R-factor:
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0.218
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R-free:
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0.269
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Authors:
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L.-W.Hung,E.L.Holbrook,S.R.Holbrook
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Key ref:
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L.W.Hung
et al.
(2000).
The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
Proc Natl Acad Sci U S A,
97,
5107-5112.
PubMed id:
DOI:
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Date:
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18-Jan-00
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Release date:
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16-May-00
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Headers
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References
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G-C-U-G-G-G-C-G-C-A-G-G
12 bases
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C-C-U-G-A-C-G-G-U-A-C-A-G-C
14 bases
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G-C-U-G-G-G-C-G-C-A-G-G
12 bases
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C-C-U-G-A-C-G-G-U-A-C-A-G-C
14 bases
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G-C-U-G-G-G-C-G-C-A-G-G
12 bases
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C-C-U-G-A-C-G-G-U-A-C-A-G-C
14 bases
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G-C-U-G-G-G-C-G-C-A-G-G
12 bases
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C-C-U-G-A-C-G-G-U-A-C-A-G-C
14 bases
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DOI no:
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Proc Natl Acad Sci U S A
97:5107-5112
(2000)
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PubMed id:
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The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
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L.W.Hung,
E.L.Holbrook,
S.R.Holbrook.
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ABSTRACT
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The crystal and molecular structure of an RNA duplex corresponding to the high
affinity Rev protein binding element (RBE) has been determined at 2.1-A
resolution. Four unique duplexes are present in the crystal, comprising two
structural variants. In each duplex, the RNA double helix consists of an
annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of
G-G and G-A noncanonical base pairs and a flipped-out uridine. The 12-mer strand
has an A-form conformation, whereas the 14-mer strand is distorted to
accommodate the bulges and noncanonical base pairing. In contrast to the NMR
model of the unbound RBE, an asymmetric G-G pair with N2-N7 and N1-O6 hydrogen
bonding, is formed in each helix. The G-A base pairing agrees with the NMR
structure in one structural variant, but forms a novel water-mediated pair in
the other. A backbone flip and reorientation of the G-G base pair is required to
assume the RBE conformation present in the NMR model of the complex between the
RBE and the Rev peptide.
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Selected figure(s)
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Figure 2.
Fig. 2. Stereo view of the least-squares superposition of
type I (black) and type II (red) helices viewed perpendicular to
the helix axis and into the major groove of the internal loop.
The bulged nucleotides A21 and U25 protrude from the helix. The
helical axes are bent by  17° for
type I and 8° for
type II duplexes.
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Figure 6.
Fig. 6. Stacking interactions between base pairs in and
around the duplex 1 RBE internal loop viewed perpendicular to
the base pair plane. (a) G104-C127 and G105-A126. (b) G105-A126
and G106-G124. (c) G106-G124 and C107-G123.
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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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N.K.Ngandu,
K.Scheffler,
P.Moore,
Z.Woodman,
D.Martin,
and
C.Seoighe
(2008).
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.
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Virol J,
5,
160.
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W.Rypniewski,
D.A.Adamiak,
J.Milecki,
and
R.W.Adamiak
(2008).
Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.
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RNA,
14,
1845-1851.
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PDB codes:
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Y.Timsit,
and
S.Bombard
(2007).
The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.
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RNA,
13,
2098-2107.
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PDB codes:
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B.Pan,
K.Shi,
and
M.Sundaralingam
(2006).
Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.
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Proc Natl Acad Sci U S A,
103,
3130-3134.
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PDB code:
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N.Carrasco,
Y.Buzin,
E.Tyson,
E.Halpert,
and
Z.Huang
(2004).
Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion.
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Nucleic Acids Res,
32,
1638-1646.
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B.Pan,
Y.Xiong,
K.Shi,
and
M.Sundaralingam
(2003).
Crystal structure of a bulged RNA tetraplex at 1.1 a resolution: implications for a novel binding site in RNA tetraplex.
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Structure,
11,
1423-1430.
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PDB code:
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N.W.Luedtke,
and
Y.Tor
(2003).
Fluorescence-based methods for evaluating the RNA affinity and specificity of HIV-1 Rev-RRE inhibitors.
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Biopolymers,
70,
103-119.
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V.Kacer,
S.A.Scaringe,
J.N.Scarsdale,
and
J.P.Rife
(2003).
Crystal structures of r(GGUCACAGCCC)2.
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Acta Crystallogr D Biol Crystallogr,
59,
423-432.
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PDB codes:
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E.A.Lesnik,
R.Sampath,
and
D.J.Ecker
(2002).
Rev response elements (RRE) in lentiviruses: an RNAMotif algorithm-based strategy for RRE prediction.
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Med Res Rev,
22,
617-636.
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E.Ennifar,
P.Carpentier,
J.L.Ferrer,
P.Walter,
and
P.Dumas
(2002).
X-ray-induced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing.
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Acta Crystallogr D Biol Crystallogr,
58,
1262-1268.
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V.Tereshko,
S.T.Wallace,
N.Usman,
F.E.Wincott,
and
M.Egli
(2001).
X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
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RNA,
7,
405-420.
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PDB codes:
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M.E.Burkard,
and
D.H.Turner
(2000).
NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.
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Biochemistry,
39,
11748-11762.
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PDB codes:
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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
codes are
shown on the right.
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