5ykx: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-==The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Zn ions==
+==The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion==
-<StructureSection load='5ykx' size='340' side='right' caption='[[5ykx]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5ykx' size='340' side='right'caption='[[5ykx]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ykx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ykx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Macrobrachium_rosenbergii_nodavirus Macrobrachium rosenbergii nodavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YKX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 2&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ykx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykx OCA], [http://pdbe.org/5ykx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykx RCSB], [http://www.ebi.ac.uk/pdbsum/5ykx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykx 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=5ykx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykx OCA], [https://pdbe.org/5ykx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ykx RCSB], [https://www.ebi.ac.uk/pdbsum/5ykx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6XNL3_MRNV Q6XNL3_MRNV]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
+The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.,Chen NC, Yoshimura M, Miyazaki N, Guan HH, Chuankhayan P, Lin CC, Chen SK, Lin PJ, Huang YC, Iwasaki K, Nakagawa A, Chan SI, Chen CJ Commun Biol. 2019 Feb 20;2:72. doi: 10.1038/s42003-019-0311-z. eCollection 2019. PMID:30820467<ref>PMID:30820467</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5ykx" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Chen, C J]]
+[[Category: Large Structures]]
-[[Category: Chen, N C]]
+[[Category: Macrobrachium rosenbergii nodavirus]]
-[[Category: Chuankhayan, P]]
+[[Category: Chen CJ]]
-[[Category: Guan, H H]]
+[[Category: Chen NC]]
-[[Category: Lin, C C]]
+[[Category: Chuankhayan P]]
-[[Category: Yoshimura, M]]
+[[Category: Guan HH]]
-[[Category: Viral capsid protein]]
+[[Category: Lin CC]]
-[[Category: Viral protein]]
+[[Category: Yoshimura M]]