2rfk

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[[Image:2rfk.jpg|left|200px]]
 
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==Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex==
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The line below this paragraph, containing "STRUCTURE_2rfk", creates the "Structure Box" on the page.
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<StructureSection load='2rfk' size='340' side='right'caption='[[2rfk]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2rfk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RFK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.87&#8491;</td></tr>
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<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>
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{{STRUCTURE_2rfk| PDB=2rfk | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rfk OCA], [https://pdbe.org/2rfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rfk RCSB], [https://www.ebi.ac.uk/pdbsum/2rfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rfk ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rf/2rfk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2rfk ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The most complex RNA pseudouridylases are H/ACA ribonucleoprotein particles, which use a guide RNA for substrate capture and four proteins (Cbf5, Nop10, Gar1 and L7Ae/NHP2) for substrate modification. Here we report the three-dimensional structure of a catalytically deficient archaeal enzyme complex (including the guide RNA and three of the four essential proteins) bound to a substrate RNA. Extensive interactions of Cbf5 with one guide-substrate helix and a guide RNA stem shape the forked guide-substrate RNA complex structure and position the substrate in proximity of the Cbf5 catalytic center. Our structural and complementary fluorescence analyses also indicate that precise placement of the target uridine at the active site requires a conformation of the guide-substrate RNA duplex that is brought about by the previously identified concurrent interaction of the guide RNA with L7Ae and a composite Cbf5-Nop10 surface, and further identify a residue that is critical in this process.
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'''Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex'''
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Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex.,Liang B, Xue S, Terns RM, Terns MP, Li H Nat Struct Mol Biol. 2007 Dec 2. PMID:18059286<ref>PMID:18059286</ref>
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==Overview==
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The most complex RNA pseudouridylases are H/ACA ribonucleoprotein particles, which use a guide RNA for substrate capture and four proteins (Cbf5, Nop10, Gar1 and L7Ae/NHP2) for substrate modification. Here we report the three-dimensional structure of a catalytically deficient archaeal enzyme complex (including the guide RNA and three of the four essential proteins) bound to a substrate RNA. Extensive interactions of Cbf5 with one guide-substrate helix and a guide RNA stem shape the forked guide-substrate RNA complex structure and position the substrate in proximity of the Cbf5 catalytic center. Our structural and complementary fluorescence analyses also indicate that precise placement of the target uridine at the active site requires a conformation of the guide-substrate RNA duplex that is brought about by the previously identified concurrent interaction of the guide RNA with L7Ae and a composite Cbf5-Nop10 surface, and further identify a residue that is critical in this process.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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2RFK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RFK OCA].
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</div>
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<div class="pdbe-citations 2rfk" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex., Liang B, Xue S, Terns RM, Terns MP, Li H, Nat Struct Mol Biol. 2007 Dec 2;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18059286 18059286]
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*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
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[[Category: Protein complex]]
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*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
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*[[Ribosome biogenesis protein 3D structures|Ribosome biogenesis protein 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Li, H.]]
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[[Category: Li H]]
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[[Category: Liang, B.]]
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[[Category: Liang B]]
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[[Category: SECSG, Southeast Collaboratory for Structural Genomics.]]
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[[Category: Terns MP]]
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[[Category: Terns, M P.]]
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[[Category: Terns RM]]
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[[Category: Terns, R M.]]
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[[Category: Xue S]]
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[[Category: Xue, S.]]
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[[Category: Archaeal h/aca ribonucleoprotein complex]]
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[[Category: Isomerase]]
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[[Category: Isomerase/rna complex]]
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[[Category: Protein-rna complex]]
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[[Category: Ribosome biogenesis]]
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[[Category: Rrna processing]]
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[[Category: Secsg]]
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[[Category: Southeast collaboratory for structural genomic]]
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[[Category: Structural genomic]]
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[[Category: Trna processing]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 16:49:21 2008''
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Current revision

Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex

PDB ID 2rfk

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