2ec7: Difference between revisions

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 ==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==
-<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''>
+<StructureSection load='2ec7' size='340' side='right'caption='[[2ec7]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hiv-2 Hiv-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_2_(ISOLATE_GHANA-1) Human immunodeficiency virus type 2 (ISOLATE GHANA-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nc8|1nc8]], [[2e1x|2e1x]], [[2di2|2di2]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://pdbe.org/2ec7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [https://pdbe.org/2ec7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ec7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ec7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1]] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity).  Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity).  Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity).  p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity).
+[https://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity).  Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity).  Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity).  p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/2ec7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/2ec7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ec7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7.,Matsui T, Tanaka T, Endoh H, Sato K, Tanaka H, Miyauchi E, Kawashima Y, Nagai-Makabe M, Komatsu H, Kohno T, Maeda T, Kodera Y Biochemistry. 2009 May 26;48(20):4314-23. PMID:19334676<ref>PMID:19334676</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2ec7" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Gag polyprotein|Gag polyprotein]]
+*[[Gag polyprotein 3D structures|Gag polyprotein 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Hiv-2]]
+[[Category: Large Structures]]
-[[Category: Endoh, H]]
+[[Category: Endoh H]]
-[[Category: Kodera, Y]]
+[[Category: Kodera Y]]
-[[Category: Kohno, T]]
+[[Category: Kohno T]]
-[[Category: Komatsu, H]]
+[[Category: Komatsu H]]
-[[Category: Maeda, T]]
+[[Category: Maeda T]]
-[[Category: Matsui, T]]
+[[Category: Matsui T]]
-[[Category: Miyauchi, E]]
+[[Category: Miyauchi E]]
-[[Category: Tanaka, H]]
+[[Category: Tanaka H]]
-[[Category: Tanaka, T]]
+[[Category: Tanaka T]]
-[[Category: Nucleocapsid protein]]
-[[Category: Rna recognition]]
-[[Category: Viral protein]]
-[[Category: Zinc finger]]