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Viral protein
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PDB id
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2ec7
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Contents |
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* Residue conservation analysis
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PDB id:
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Viral protein
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Title:
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Solution structure of human immunodificiency virus type-2 nucleocapsid protein
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Structure:
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Gag polyprotein (pr55gag). Chain: a. Fragment: cchc-type 1, cchc-type 2. Synonym: nucleocapsid protein (ncp8). Engineered: yes
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Source:
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Human immunodeficiency virus type 2 (isolate ghana-1). Organism_taxid: 11717. Strain: isolate ghana-1 subtype a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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NMR struc:
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11 models
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Authors:
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T.Matsui,Y.Kodera,T.Tanaka,H.Endoh,H.Tanaka,E.Miyauchi, H.Komatsu,T.Kohno,T.Maeda
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Key ref:
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T.Matsui
et al.
(2009).
The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7.
Biochemistry,
48,
4314-4323.
PubMed id:
DOI:
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Date:
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10-Feb-07
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Release date:
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19-Feb-08
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PROCHECK
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Headers
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References
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P18041
(GAG_HV2G1) -
Gag polyprotein
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Seq:
Struc:
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522 a.a.
49 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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Gene Ontology (GO) functional annotation
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Biochemical function
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nucleic acid binding
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2 terms
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DOI no:
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Biochemistry
48:4314-4323
(2009)
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PubMed id:
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The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7.
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T.Matsui,
T.Tanaka,
H.Endoh,
K.Sato,
H.Tanaka,
E.Miyauchi,
Y.Kawashima,
M.Nagai-Makabe,
H.Komatsu,
T.Kohno,
T.Maeda,
Y.Kodera.
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ABSTRACT
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The nucleocapsid (NC) protein of HIV, which contains two CCHC-type zinc fingers
connected by a linker, is a multi-functional protein involved in many of the
critical steps of the HIV life cycle. HIV-1 and HIV-2 contain the NC proteins
NCp7 and NCp8, respectively. The amino acid sequences of both NC proteins are
67% identical. For NCp7, the important elements for RNA binding were found to be
the first zinc finger flanked by the linker, as the minimal active domain, and
the 3<sub>10</sub> helix in the N-terminus, as the secondary active
domain. However, for the NCp8 counterpart in HIV-2, the binding mechanism to
viral RNA has not yet been clarified. In this study, we determined NCp8's
three-dimensional structure for the first time and examined the dynamic behavior
and chemical shift perturbation as a function of the concentration of the viral
RNA SL3. Moreover, the specific binding activities of NCp8 and the NCp8-derived
peptides with SL3 were examined by native polyacrylamide gel electrophoresis
assay. These results indicate that the RNA recognition mechanism for NCp8 is
different from that of NCp7 and that the hydrophobic cleft in the second zinc
finger acts as a secondary active domain instead of the
3<sub>10</sub> helix in NCp7. Furthermore, the flexibility of the
linker is limited by the hydrogen bond between the first zinc finger (Asn11) and
the linker (Arg27), which makes it possible for the sites around Trp10 in the
minimal active domain and the secondary active domain to form the binding
surface.
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Links
