2r02: Difference between revisions

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 ==Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLTSL Late Domain==
-<StructureSection load='2r02' size='340' side='right' caption='[[2r02]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='2r02' size='340' side='right'caption='[[2r02]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r02]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R02 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r02]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/HIV-1_M:J_SE9173 HIV-1 M:J_SE9173] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R02 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2r03|2r03]], [[2r05|2r05]]</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]] 2.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDCD6IP, AIP1, ALIX, KIAA1375 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2r02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r02 OCA], [https://pdbe.org/2r02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r02 RCSB], [https://www.ebi.ac.uk/pdbsum/2r02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r02 ProSAT]</span></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=2r02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r02 OCA], [http://pdbe.org/2r02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r02 RCSB], [http://www.ebi.ac.uk/pdbsum/2r02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r02 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PDC6I_HUMAN PDC6I_HUMAN]] Class E VPS protein involved in concentration and sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome. Binds to the phospholipid lysobisphosphatidic acid (LBPA) which is abundant in MVBs internal membranes. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses). Appears to be an adapter for a subset of ESCRT-III proteins, such as CHMP4, to function at distinct membranes. Required for completion of cytokinesis. Involved in HIV-1 virus budding. Can replace TSG101 it its role of supporting HIV-1 release; this function implies the interaction with CHMP4B. May play a role in the regulation of both apoptosis and cell proliferation.<ref>PMID:14505569</ref> <ref>PMID:14505570</ref> <ref>PMID:14739459</ref> <ref>PMID:17853893</ref> <ref>PMID:17428861</ref> <ref>PMID:17556548</ref>  [[http://www.uniprot.org/uniprot/GAG_HV1S9 GAG_HV1S9]] Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu (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/PDC6I_HUMAN PDC6I_HUMAN] Class E VPS protein involved in concentration and sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome. Binds to the phospholipid lysobisphosphatidic acid (LBPA) which is abundant in MVBs internal membranes. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses). Appears to be an adapter for a subset of ESCRT-III proteins, such as CHMP4, to function at distinct membranes. Required for completion of cytokinesis. Involved in HIV-1 virus budding. Can replace TSG101 it its role of supporting HIV-1 release; this function implies the interaction with CHMP4B. May play a role in the regulation of both apoptosis and cell proliferation.<ref>PMID:14505569</ref> <ref>PMID:14505570</ref> <ref>PMID:14739459</ref> <ref>PMID:17853893</ref> <ref>PMID:17428861</ref> <ref>PMID:17556548</ref>
 == 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/r0/2r02_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r0/2r02_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 19: @@
 </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=2r02 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Retrovirus budding requires short peptide motifs (late domains) located within the viral Gag protein that function by recruiting cellular factors. The YPX(n)L late domains of HIV and other lentiviruses recruit the protein ALIX (also known as AIP1), which also functions in vesicle formation at the multivesicular body and in the abscission stage of cytokinesis. Here, we report the crystal structures of ALIX in complex with the YPX(n)L late domains from HIV-1 and EIAV. The two distinct late domains bind at the same site on the ALIX V domain but adopt different conformations that allow them to make equivalent contacts. Binding studies and functional assays verified the importance of key interface residues and revealed that binding affinities are tuned by context-dependent effects. These results reveal how YPX(n)L late domains recruit ALIX to facilitate virus budding and how ALIX can bind YPX(n)L sequences with both n = 1 and n = 3.
-Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV.,Zhai Q, Fisher RD, Chung HY, Myszka DG, Sundquist WI, Hill CP Nat Struct Mol Biol. 2008 Jan;15(1):43-9. Epub 2007 Dec 9. PMID:18066081<ref>PMID:18066081</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2r02" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: HIV-1 M:J_SE9173]]
-[[Category: Fisher, R D]]
+[[Category: Homo sapiens]]
-[[Category: Hill, C P]]
+[[Category: Large Structures]]
-[[Category: Zhai, Q]]
+[[Category: Fisher RD]]
-[[Category: Aid]]
+[[Category: Hill CP]]
-[[Category: Apoptosis]]
+[[Category: Zhai Q]]
-[[Category: Capsid protein]]
-[[Category: Coiled-coil]]
-[[Category: Cytoplasm]]
-[[Category: Host-virus interaction]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Myristate]]
-[[Category: Nucleus]]
-[[Category: Phosphorylation]]
-[[Category: Polymorphism]]
-[[Category: Protein transport]]
-[[Category: Rna-binding]]
-[[Category: Transport]]
-[[Category: Viral nucleoprotein]]
-[[Category: Virion]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]