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PDBsum entry 2ec7
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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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| Name: |
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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:
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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 from Human immunodeficiency virus type 2 subtype A (isolate Ghana-1)
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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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CATH domain |
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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 multifunctional protein involved in many of the
critical steps of the HIV life cycle. HIV-1 and HIV-2 contain 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(10) helix in the N-terminus, as the secondary active domain. However, for the
NCp8 counterpart in HIV-2, the mechanism for binding 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 viral RNA SL3. Moreover, the
specific binding activities of NCp8 and the NCp8-derived peptides with SL3 were
examined by a 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(10) 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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