1khv: 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: @@
-{{Seed}}
-[[Image:1khv.png|left|200px]]
-<!--
+==Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Lu3+==
-The line below this paragraph, containing "STRUCTURE_1khv", creates the "Structure Box" on the page.
+<StructureSection load='1khv' size='340' side='right'caption='[[1khv]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1khv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rabbit_hemorrhagic_disease_virus Rabbit hemorrhagic disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KHV FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene></td></tr>
-{{STRUCTURE_1khv|  PDB=1khv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1khv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khv OCA], [https://pdbe.org/1khv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1khv RCSB], [https://www.ebi.ac.uk/pdbsum/1khv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1khv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_RHDVF POLG_RHDVF] NTPase presumably plays a role in replication (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref>   Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref>   3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref>   RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref>   Capsid protein VP60 self assembles to form an icosahedral capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate VP2 proteins and genomic or subgenomic RNA. Attaches virion to target cells by binding histo-blood group antigens, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</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/kh/1khv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1khv ConSurf].
+<div style="clear:both"></div>
-===Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Lu3+===
+==See Also==
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_11677245}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 11677245 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Large Structures]]
-{{ABSTRACT_PUBMED_11677245}}
-==About this Structure==
-KHV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rabbit_hemorrhagic_disease_virus Rabbit hemorrhagic disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHV OCA].
-==Reference==
-Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase., Ng KK, Cherney MM, Vazquez AL, Machin A, Alonso JM, Parra F, James MN, J Biol Chem. 2002 Jan 11;277(2):1381-7. Epub 2001 Oct 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11677245 11677245]
-[[Category: RNA-directed RNA polymerase]]
 [[Category: Rabbit hemorrhagic disease virus]]
-[[Category: Single protein]]
+[[Category: Alonso JM]]
-[[Category: Alonso, J M.]]
+[[Category: Cherney MM]]
-[[Category: Cherney, M M.]]
+[[Category: James MN]]
-[[Category: James, M N.]]
+[[Category: Machin A]]
-[[Category: Machin, A.]]
+[[Category: Ng KK]]
-[[Category: Ng, K K.]]
+[[Category: Parra F]]
-[[Category: Parra, F.]]
+[[Category: Vazquez AL]]
-[[Category: Vazquez, A L.]]
-[[Category: Rna-dependent rna polymerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 10:22:18 2008''