2j7n: 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:2j7n.jpg|left|200px]]
- {{Structure
+==Structure of the RNAi polymerase from Neurospora crassa==
-|PDB= 2j7n |SIZE=350|CAPTION= <scene name='initialview01'>2j7n</scene>, resolution 2.30&Aring;
+<StructureSection load='2j7n' size='340' side='right'caption='[[2j7n]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Gol+Binding+Site+For+Chain+B'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+<table><tr><td colspan='2'>[[2j7n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7N FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2j7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7n OCA], [https://pdbe.org/2j7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j7n RCSB], [https://www.ebi.ac.uk/pdbsum/2j7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7n ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9Y7G6_NEUCS Q9Y7G6_NEUCS]
+== 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/j7/2j7n_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=2j7n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant single-stranded RNA. We report the 2.3-A resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, and find that it forms a relatively compact dimeric molecule, each subunit of which comprises several domains with, at its core, a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription. This evolutionary link between the two enzyme types suggests that aspects of RNA silencing in some organisms may recapitulate transcription/replication pathways functioning in the ancient RNA-based world.
-'''STRUCTURE OF THE RNAI POLYMERASE FROM NEUROSPORA CRASSA'''
+The structure of an RNAi polymerase links RNA silencing and transcription.,Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM PLoS Biol. 2006 Dec;4(12):e434. PMID:17147473<ref>PMID:17147473</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2j7n" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant single-stranded RNA. We report the 2.3-A resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, and find that it forms a relatively compact dimeric molecule, each subunit of which comprises several domains with, at its core, a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription. This evolutionary link between the two enzyme types suggests that aspects of RNA silencing in some organisms may recapitulate transcription/replication pathways functioning in the ancient RNA-based world.
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-J7N is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7N OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-The structure of an RNAi polymerase links RNA silencing and transcription., Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM, PLoS Biol. 2006 Dec;4(12):e434. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17147473 17147473]
 [[Category: Neurospora crassa]]
-[[Category: Single protein]]
+[[Category: Bamford DH]]
-[[Category: Bamford, D H.]]
+[[Category: Grimes JM]]
-[[Category: Grimes, J M.]]
+[[Category: Koivunen MRL]]
-[[Category: Koivunen, M R.L.]]
+[[Category: Makeyev EV]]
-[[Category: Makeyev, E V.]]
+[[Category: Salgado PS]]
-[[Category: Salgado, P S.]]
+[[Category: Stuart DI]]
-[[Category: Stuart, D I.]]
-[[Category: GOL]]
-[[Category: MG]]
-[[Category: hydrolase]]
-[[Category: hypothetical protein]]
-[[Category: rna dependent rna polymerase]]
-[[Category: rna-directed rna polymerase]]
-[[Category: rnai response]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:38:19 2008''