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1u6p

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[[Image:1u6p.gif|left|200px]]<br /><applet load="1u6p" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1u6p" />
 
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'''NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein'''<br />
 
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==Overview==
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==NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein==
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All retroviruses specifically package two copies of their genomes during virus assembly, a requirement for strand-transfer-mediated recombination during reverse transcription. Genomic RNA exists in virions as dimers, and the overlap of RNA elements that promote dimerization and encapsidation suggests that these processes may be coupled. Both processes are mediated by the nucleocapsid domain (NC) of the retroviral Gag polyprotein. Here we show that dimerization-induced register shifts in base pairing within the Psi-RNA packaging signal of Moloney murine leukaemia virus (MoMuLV) expose conserved UCUG elements that bind NC with high affinity (dissociation constant = 75 +/- 12 nM). These elements are base-paired and do not bind NC in the monomeric RNA. The structure of the NC complex with a 101-nucleotide 'core encapsidation' segment of the MoMuLV Psi site reveals a network of interactions that promote sequence- and structure-specific binding by NC's single CCHC zinc knuckle. Our findings support a structural RNA switch mechanism for genome encapsidation, in which protein binding sites are sequestered by base pairing in the monomeric RNA and become exposed upon dimerization to promote packaging of a diploid genome.
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<StructureSection load='1u6p' size='340' side='right'caption='[[1u6p]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1u6p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U6P FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP7:N1-PROTONATED+ADENOSINE-5-MONOPHOSPHATE'>AP7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u6p OCA], [https://pdbe.org/1u6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u6p RCSB], [https://www.ebi.ac.uk/pdbsum/1u6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u6p ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GAG_MLVMS GAG_MLVMS] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release.<ref>PMID:19864377</ref> Matrix protein p15 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 (By similarity).<ref>PMID:19864377</ref> Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity).<ref>PMID:19864377</ref> Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization.<ref>PMID:19864377</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u6/1u6p_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1u6p ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1U6P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U6P OCA].
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*[[Gag polyprotein 3D structures|Gag polyprotein 3D structures]]
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*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
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==Reference==
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== References ==
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Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus., D'Souza V, Summers MF, Nature. 2004 Sep 30;431(7008):586-90. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15457265 15457265]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Moloney murine leukemia virus]]
[[Category: Moloney murine leukemia virus]]
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[[Category: Single protein]]
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[[Category: D'Souza V]]
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[[Category: Souza, V D.]]
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[[Category: Summers MF]]
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[[Category: Summers, M F.]]
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[[Category: ZN]]
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[[Category: a-c mismatch]]
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[[Category: a-minor k-turn]]
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[[Category: bulge]]
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[[Category: g-a mismatch]]
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[[Category: g-u mismatch]]
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[[Category: mlv]]
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[[Category: nc]]
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[[Category: stem loop]]
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[[Category: u-u mismatch]]
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[[Category: zinc finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:21:07 2008''
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Current revision

NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein

PDB ID 1u6p

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