1vby

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{{Seed}}
 
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[[Image:1vby.png|left|200px]]
 
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==Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound==
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The line below this paragraph, containing "STRUCTURE_1vby", creates the "Structure Box" on the page.
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<StructureSection load='1vby' size='340' side='right'caption='[[1vby]], [[Resolution|resolution]] 2.90&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'>[[1vby]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBY 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]] 2.9&#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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_1vby| PDB=1vby | 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=1vby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vby OCA], [https://pdbe.org/1vby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vby RCSB], [https://www.ebi.ac.uk/pdbsum/1vby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vby ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
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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/vb/1vby_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1vby 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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Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.
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===Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound===
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A conformational switch controls hepatitis delta virus ribozyme catalysis.,Ke A, Zhou K, Ding F, Cate JH, Doudna JA Nature. 2004 May 13;429(6988):201-5. PMID:15141216<ref>PMID:15141216</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1vby" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15141216}}, adds the Publication Abstract to the page
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*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15141216 is the PubMed ID number.
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_15141216}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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1VBY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBY OCA].
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==Reference==
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A conformational switch controls hepatitis delta virus ribozyme catalysis., Ke A, Zhou K, Ding F, Cate JH, Doudna JA, Nature. 2004 May 13;429(6988):201-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15141216 15141216]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cate, J H.D.]]
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[[Category: Cate JHD]]
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[[Category: Ding, F.]]
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[[Category: Ding F]]
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[[Category: Doudna, J A.]]
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[[Category: Doudna JA]]
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[[Category: Ke, A.]]
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[[Category: Ke A]]
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[[Category: Zhou, K.]]
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[[Category: Zhou K]]
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[[Category: Hdv]]
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[[Category: Precursor]]
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[[Category: Ribozyme]]
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[[Category: Rna]]
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[[Category: U1a]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 16:37:25 2008''
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Current revision

Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound

PDB ID 1vby

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