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==Crystal Structure of the Rotavirus Double Layered Particle==
==Crystal Structure of the Rotavirus Double Layered Particle==
<StructureSection load='3kz4' size='340' side='right' caption='[[3kz4]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
<SX load='3kz4' size='340' side='right' viewer='molstar' caption='[[3kz4]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3kz4]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KZ4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3kz4]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_rotavirus_strain_UK/G6 Bovine rotavirus strain UK/G6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KZ4 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">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gzt|3gzt]], [[3gzu|3gzu]], [[3fmg|3fmg]]</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=3kz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kz4 OCA], [http://pdbe.org/3kz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kz4 RCSB], [http://www.ebi.ac.uk/pdbsum/3kz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kz4 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=3kz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kz4 OCA], [https://pdbe.org/3kz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kz4 RCSB], [https://www.ebi.ac.uk/pdbsum/3kz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kz4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/VP6_ROTBN VP6_ROTBN]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP (By similarity).  
[https://www.uniprot.org/uniprot/VP2_ROTBU VP2_ROTBU] Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle (PubMed:20122940). It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core (PubMed:20122940). The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus (PubMed:20122940). Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini (PubMed:20122940). VP2 is required for the replicase activity of VP1 polymerase (By similarity). Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles (PubMed:20122940). May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication (By similarity).[HAMAP-Rule:MF_04127]<ref>PMID:20122940</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kz/3kz4_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kz/3kz4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 20: 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=3kz4 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=3kz4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The rotavirus inner capsid particle, known as the "double-layered particle" (DLP), is the "payload" delivered into a cell in the process of viral infection. Its inner and outer protein layers, composed of viral protein (VP) 2 and VP6, respectively, package the 11 segments of the double-stranded RNA (dsRNA) of the viral genome, as well as about the same number of polymerase molecules (VP1) and capping-enzyme molecules (VP3). We have determined the crystal structure of the bovine rotavirus DLP. There is one full particle (outer diameter approximately 700 A) in the asymmetric unit of the P2(1)2(1)2(1) unit cell of dimensions a=740 A, b=1198 A, and c=1345 A. A three-dimensional reconstruction from electron cryomicroscopy was used as a molecular replacement model for initial phase determination to about 18.5 A resolution, and the 60-fold redundancy of icosahedral particle symmetry allowed phases to be extended stepwise to the limiting resolution of the data (3.8 A). The structure of a VP6 trimer (determined previously by others) fits the outer layer density with very little adjustment. The T=13 triangulation number of that layer implies that there are four and one-third VP6 trimers per icosahedral asymmetric unit. The inner layer has 120 copies of VP2 and thus 2 copies per icosahedral asymmetric unit, designated VP2A and VP2B. Residues 101-880 fold into a relatively thin principal domain, comma-like in outline, shaped such that only rather modest distortions (concentrated at two "subdomain" boundaries) allow VP2A and VP2B to form a uniform layer with essentially no gaps at the subunit boundaries, except for a modest pore along the 5-fold axis. The VP2 principal domain resembles those of the corresponding shells and homologous proteins in other dsRNA viruses: lambda1 in orthoreoviruses and VP3 in orbiviruses. Residues 1-80 of VP2A and VP2B fold together with four other such pairs into a "5-fold hub" that projects into the DLP interior along the 5-fold axis; residues 81-100 link the 10 polypeptide chains emerging from a 5-fold hub to the N-termini of their corresponding principal domains, clustered into a decameric assembly unit. The 5-fold hub appears to have several distinct functions. One function is to recruit a copy of VP1 (or of a VP1-VP3 complex), potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. The second function is to serve as a shaft around which can coil a segment of dsRNA. The third function is to guide nascent mRNA, synthesized in the DLP interior by VP1 and 5'-capped by the action of VP3, out through a 5-fold exit channel. We propose a model for rotavirus particle assembly, based on known requirements for virion formation, together with the structure of the DLP and that of VP1, determined earlier.


X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.,McClain B, Settembre E, Temple BR, Bellamy AR, Harrison SC J Mol Biol. 2010 Mar 26;397(2):587-99. Epub 2010 Feb 1. PMID:20122940<ref>PMID:20122940</ref>
==See Also==
 
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3kz4" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</SX>
[[Category: Bellamy, A R]]
[[Category: Bovine rotavirus strain UK/G6]]
[[Category: Harrison, S C]]
[[Category: Large Structures]]
[[Category: Mcclain, B]]
[[Category: Bellamy AR]]
[[Category: Settembre, E C]]
[[Category: Harrison SC]]
[[Category: Capsid]]
[[Category: Mcclain B]]
[[Category: Core protein]]
[[Category: Settembre EC]]
[[Category: Dsrna virus]]
[[Category: Icosahedral virus]]
[[Category: Metal-binding]]
[[Category: Rna-binding]]
[[Category: Rotavirus]]
[[Category: Virion]]
[[Category: Virus]]
[[Category: Zinc]]

Latest revision as of 10:18, 21 February 2024

Crystal Structure of the Rotavirus Double Layered Particle

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