2r8s

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{{Seed}}
 
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[[Image:2r8s.png|left|200px]]
 
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==High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain==
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The line below this paragraph, containing "STRUCTURE_2r8s", creates the "Structure Box" on the page.
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<StructureSection load='2r8s' size='340' side='right'caption='[[2r8s]], [[Resolution|resolution]] 1.95&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'>[[2r8s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8S 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]] 1.95&#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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_2r8s| PDB=2r8s | 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=2r8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8s OCA], [https://pdbe.org/2r8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8s RCSB], [https://www.ebi.ac.uk/pdbsum/2r8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8s ProSAT]</span></td></tr>
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</table>
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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/r8/2r8s_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=2r8s 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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Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab-RNA complex at 1.95 A. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab-RNA interface also differs significantly from Fab-protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology.
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===High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain===
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Synthetic antibodies for specific recognition and crystallization of structured RNA.,Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):82-7. Epub 2007 Dec 27. PMID:18162543<ref>PMID:18162543</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 2r8s" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18162543}}, adds the Publication Abstract to the page
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*[[Antibody 3D structures|Antibody 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18162543 is the PubMed ID number.
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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{{ABSTRACT_PUBMED_18162543}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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2R8S is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8S OCA].
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</StructureSection>
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[[Category: Large Structures]]
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==Reference==
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Synthetic antibodies for specific recognition and crystallization of structured RNA., Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA, Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):82-7. Epub 2007 Dec 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18162543 18162543]
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[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Protein complex]]
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[[Category: Koide S]]
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[[Category: Koide, S.]]
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[[Category: Kossiakoff AA]]
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[[Category: Kossiakoff, A A.]]
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[[Category: Piccirilli JA]]
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[[Category: Piccirilli, J A.]]
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[[Category: Sidhu SS]]
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[[Category: Sidhu, S S.]]
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[[Category: Tereshko V]]
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[[Category: Tereshko, V.]]
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[[Category: Ye JD]]
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[[Category: Ye, J D.]]
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[[Category: Fab-rna complex]]
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[[Category: Immune system/rna complex]]
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[[Category: Protein-rna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:10:27 2008''
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Current revision

High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain

PDB ID 2r8s

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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