2r05: Difference between revisions

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<StructureSection load='2r05' size='340' side='right'caption='[[2r05]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
<StructureSection load='2r05' size='340' side='right'caption='[[2r05]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2r05]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R05 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2r05]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(isolate_YU2) Human immunodeficiency virus type 1 (isolate YU2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R05 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2r02|2r02]], [[2r03|2r03]]</div></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]] 2.55&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDCD6IP, AIP1, ALIX, KIAA1375 ([https://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=2r05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r05 OCA], [https://pdbe.org/2r05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r05 RCSB], [https://www.ebi.ac.uk/pdbsum/2r05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r05 ProSAT]</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=2r05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r05 OCA], [https://pdbe.org/2r05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r05 RCSB], [https://www.ebi.ac.uk/pdbsum/2r05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r05 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[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> [[https://www.uniprot.org/uniprot/GAG_HV1Y2 GAG_HV1Y2]] 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.  Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.  Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers.  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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[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=2r05 ConSurf].
</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=2r05 ConSurf].
<div style="clear:both"></div>
<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 2r05" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Fisher, R D]]
[[Category: Fisher RD]]
[[Category: Hill, C P]]
[[Category: Hill CP]]
[[Category: Zhai, Q]]
[[Category: Zhai Q]]
[[Category: Aid]]
[[Category: Apoptosis]]
[[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]]

Latest revision as of 12:19, 21 February 2024

Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late DomainCrystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain

Structural highlights

2r05 is a 2 chain structure with sequence from Homo sapiens and Human immunodeficiency virus type 1 (isolate YU2). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.55Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3] [4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Strack B, Calistri A, Craig S, Popova E, Gottlinger HG. AIP1/ALIX is a binding partner for HIV-1 p6 and EIAV p9 functioning in virus budding. Cell. 2003 Sep 19;114(6):689-99. PMID:14505569
  2. ↑ von Schwedler UK, Stuchell M, Muller B, Ward DM, Chung HY, Morita E, Wang HE, Davis T, He GP, Cimbora DM, Scott A, Krausslich HG, Kaplan J, Morham SG, Sundquist WI. The protein network of HIV budding. Cell. 2003 Sep 19;114(6):701-13. PMID:14505570
  3. ↑ Matsuo H, Chevallier J, Mayran N, Le Blanc I, Ferguson C, Faure J, Blanc NS, Matile S, Dubochet J, Sadoul R, Parton RG, Vilbois F, Gruenberg J. Role of LBPA and Alix in multivesicular liposome formation and endosome organization. Science. 2004 Jan 23;303(5657):531-4. PMID:14739459 doi:10.1126/science.1092425
  4. ↑ Morita E, Sandrin V, Chung HY, Morham SG, Gygi SP, Rodesch CK, Sundquist WI. Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis. EMBO J. 2007 Oct 3;26(19):4215-27. Epub 2007 Sep 13. PMID:17853893 doi:10.1038/sj.emboj.7601850
  5. ↑ Usami Y, Popov S, Gottlinger HG. Potent rescue of human immunodeficiency virus type 1 late domain mutants by ALIX/AIP1 depends on its CHMP4 binding site. J Virol. 2007 Jun;81(12):6614-22. Epub 2007 Apr 11. PMID:17428861 doi:10.1128/JVI.00314-07
  6. ↑ Carlton JG, Martin-Serrano J. Parallels between cytokinesis and retroviral budding: a role for the ESCRT machinery. Science. 2007 Jun 29;316(5833):1908-12. Epub 2007 Jun 7. PMID:17556548 doi:10.1126/science.1143422

2r05, resolution 2.55Å

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