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: @@
-[[Image:1khv.jpg|left|200px]]
- {{Structure
+==Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Lu3+==
-|PDB= 1khv |SIZE=350|CAPTION= <scene name='initialview01'>1khv</scene>, resolution 2.50&Aring;
+<StructureSection load='1khv' size='340' side='right'caption='[[1khv]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=LU:LUTETIUM (III) ION'>LU</scene>
+<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>
-|ACTIVITY= [http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48]
+</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>
-|GENE=
+<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>
-}}
+<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 ==
-==Overview==
+<references/>
-The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-A resolution. The overall structure resembles a "right hand," as seen before in other polymerases, including the RdRPs of polio virus and hepatitis C virus. Two copies of the polymerase are present in the asymmetric unit of the crystal, revealing active and inactive conformations within the same crystal form. The fingers and palm domains form a relatively rigid unit, but the thumb domain can adopt either "closed" or "open" conformations differing by a rigid body rotation of approximately 8 degrees. Metal ions bind at different positions in the two conformations and suggest how structural changes may be important to enzymatic function in RdRPs. Comparisons between the structures of the alternate conformational states of rabbit hemorrhagic disease virus RdRP and the structures of RdRPs from hepatitis C virus and polio virus suggest novel structure-function relationships in this medically important class of enzymes.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-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: LU]]
-[[Category: rna-dependent rna polymerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:17:43 2008''