2a3j

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(New page: 200px<br /> <applet load="2a3j" size="450" color="white" frame="true" align="right" spinBox="true" caption="2a3j" /> '''Structure of URNdesign, a complete computat...)
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[[Image:2a3j.gif|left|200px]]<br />
 
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<applet load="2a3j" size="450" color="white" frame="true" align="right" spinBox="true"
 
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'''Structure of URNdesign, a complete computational redesign of human U1A protein'''<br />
 
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==Overview==
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==Structure of URNdesign, a complete computational redesign of human U1A protein==
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Achieving atomic-level resolution in the computational design of a protein, structure remains a challenging problem despite recent progress. Rigorous, experimental tests are needed to improve protein design algorithms, yet, studies of the structure and dynamics of computationally designed proteins, are very few. The NMR structure and backbone dynamics of a redesigned, protein of 96 amino acids are compared here with the design target, human, U1A protein. We demonstrate that the redesigned protein reproduces the, target structure to within the uncertainty of the NMR coordinates, even as, 65 out of 96 amino acids were simultaneously changed by purely, computational methods. The dynamics of the backbone of the redesigned, protein also mirror those of human U1A, suggesting that the protein design, algorithm captures the shape of the potential energy landscape in addition, to the local energy minimum.
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<StructureSection load='2a3j' size='340' side='right'caption='[[2a3j]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2a3j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A3J FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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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=2a3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a3j OCA], [https://pdbe.org/2a3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a3j RCSB], [https://www.ebi.ac.uk/pdbsum/2a3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a3j 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/a3/2a3j_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=2a3j 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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Achieving atomic-level resolution in the computational design of a protein structure remains a challenging problem despite recent progress. Rigorous experimental tests are needed to improve protein design algorithms, yet studies of the structure and dynamics of computationally designed proteins are very few. The NMR structure and backbone dynamics of a redesigned protein of 96 amino acids are compared here with the design target, human U1A protein. We demonstrate that the redesigned protein reproduces the target structure to within the uncertainty of the NMR coordinates, even as 65 out of 96 amino acids were simultaneously changed by purely computational methods. The dynamics of the backbone of the redesigned protein also mirror those of human U1A, suggesting that the protein design algorithm captures the shape of the potential energy landscape in addition to the local energy minimum.
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==About this Structure==
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High-resolution structural validation of the computational redesign of human U1A protein.,Dobson N, Dantas G, Baker D, Varani G Structure. 2006 May;14(5):847-56. PMID:16698546<ref>PMID:16698546</ref>
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2A3J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2A3J OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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High-resolution structural validation of the computational redesign of human U1A protein., Dobson N, Dantas G, Baker D, Varani G, Structure. 2006 May;14(5):847-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16698546 16698546]
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</div>
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[[Category: Homo sapiens]]
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<div class="pdbe-citations 2a3j" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Baker, D.]]
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[[Category: Dantas, G.]]
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[[Category: Dobson, N.]]
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[[Category: Varani, G.]]
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[[Category: computationally designed protein]]
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[[Category: rrm]]
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[[Category: u1a]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 20:45:44 2007''
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==See Also==
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*[[Nucleoprotein 3D structures|Nucleoprotein 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: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Baker D]]
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[[Category: Dantas G]]
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[[Category: Dobson N]]
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[[Category: Varani G]]

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Structure of URNdesign, a complete computational redesign of human U1A protein

PDB ID 2a3j

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