1cz9: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[1cz9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_sarcoma_virus Avian sarcoma virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CZ9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1asv|1asv]], [[1cxq|1cxq]], [[1cxu|1cxu]], [[1czb|1czb]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1cz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cz9 OCA], [https://pdbe.org/1cz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cz9 RCSB], [https://www.ebi.ac.uk/pdbsum/1cz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cz9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/POL_RSVP POL_RSVP]] Capsid protein p27 forms the spherical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity).  The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (By similarity).
+[https://www.uniprot.org/uniprot/POL_RSVSB POL_RSVSB] Capsid protein p27: Self-associates to form the irregular polyhedron core composed of hexamers and pentamers, that encapsulates the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro. Binds to inositol hexakisphosphate (IP6), which allows the assembly of the polyhedral capsid.[UniProtKB:P03322]  Plays a role in the oligomerization of the Gag polyprotein and in the stabilization of the immature particle. Essential layering element during tube assembly. Allows the cooperative binging of Gag to the host plasma membrane.[UniProtKB:P03322]  Binds strongly to viral nucleic acids and promotes their packaging (By similarity). Plays a role in the maturation-stabilization of the viral dimeric RNA via highly structured zinc-binding motifs (By similarity).[UniProtKB:P03322][UniProtKB:P0C776]  The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]  Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions (PubMed:9218451). This recombination event is an essential step in the viral replication cycle. Has a strong preference for using the 3'-OH at the viral DNA end as a nucleophile.[UniProtKB:P03354]<ref>PMID:9218451</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1cz9 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Six crystal structures of the core domain of integrase (IN) from avian sarcoma virus (ASV) and its active-site derivative containing an Asp64 --&gt; Asn substitution have been solved at atomic resolution ranging 1.02-1.42 A. The high-quality data provide new structural information about the active site of the enzyme and clarify previous inconsistencies in the description of this fragment. The very high resolution of the data and excellent quality of the refined models explain the dynamic properties of IN and the multiple conformations of its disordered residues. They also allow an accurate description of the solvent structure and help to locate other molecules bound to the enzyme. A detailed analysis of the flexible active-site region, in particular the loop formed by residues 144-154, suggests conformational changes which may be associated with substrate binding and enzymatic activity. The pH-dependent conformational changes of the active-site loop correlates with the pH vs activity profile observed for ASV IN.
-Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant.,Lubkowski J, Dauter Z, Yang F, Alexandratos J, Merkel G, Skalka AM, Wlodawer A Biochemistry. 1999 Oct 12;38(41):13512-22. PMID:10521258<ref>PMID:10521258</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1cz9" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 38: / Line 29: @@
 [[Category: Avian sarcoma virus]]
 [[Category: Large Structures]]
-[[Category: Alexandratos, J]]
+[[Category: Alexandratos J]]
-[[Category: Dauter, Z]]
+[[Category: Dauter Z]]
-[[Category: Lubkowski, J]]
+[[Category: Lubkowski J]]
-[[Category: Merkel, G]]
+[[Category: Merkel G]]
-[[Category: Skalka, A M]]
+[[Category: Skalka AM]]
-[[Category: Wlodawer, A]]
+[[Category: Wlodawer A]]
-[[Category: Yang, F]]
+[[Category: Yang F]]
-[[Category: Mixed beta-sheet surrounded by alpha-helice]]
-[[Category: Transferase]]