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3cfi
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3cfi is ON HOLD until Paper Publication Authors: Lam, A.Y., Pardon, E., Korotkov, K.V., Steyaert, J., Hol, W.G.J. Description: Nanobody-aided struc...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus== | |
| + | <StructureSection load='3cfi' size='340' side='right'caption='[[3cfi]], [[Resolution|resolution]] 2.58Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3cfi]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_27562 Atcc 27562] and [https://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CFI FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EpsI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 ATCC 27562]), EpsJ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 ATCC 27562]), NBEPSIJ_11 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9844 Camelus glama])</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=3cfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cfi OCA], [https://pdbe.org/3cfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cfi RCSB], [https://www.ebi.ac.uk/pdbsum/3cfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cfi ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/cf/3cfi_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=3cfi ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pseudopilins form the central pseudopilus of the sophisticated bacterial type 2 secretion systems. The crystallization of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus was greatly accelerated by the use of nanobodies, which are the smallest antigen-binding fragments derived from heavy-chain only camelid antibodies. Seven anti-EpsI:EpsJ nanobodies were generated and co-crystallization of EpsI:EpsJ nanobody complexes yielded several crystal forms very rapidly. In the structure solved, the nanobodies are arranged in planes throughout the crystal lattice, linking layers of EpsI:EpsJ heterodimers. The EpsI:EpsJ dimer observed confirms a right-handed architecture of the pseudopilus, but, compared to a previous structure of the EpsI:EpsJ heterodimer, EpsI differs 6 degrees in orientation with respect to EpsJ; one loop of EpsJ is shifted by approximately 5A due to interactions with the nanobody; and a second loop of EpsJ underwent a major change of 17A without contacts with the nanobody. Clearly, nanobodies accelerate dramatically the crystallization of recalcitrant protein complexes and can reveal conformational flexibility not observed before. | ||
| - | + | Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus.,Lam AY, Pardon E, Korotkov KV, Hol WG, Steyaert J J Struct Biol. 2009 Apr;166(1):8-15. Epub 2008 Dec 10. PMID:19118632<ref>PMID:19118632</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3cfi" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| - | + | *[[Pseudopilin|Pseudopilin]] | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Atcc 27562]] | ||
| + | [[Category: Camelus glama]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Hol, W G.J]] | ||
| + | [[Category: Korotkov, K V]] | ||
| + | [[Category: Lam, A Y]] | ||
| + | [[Category: Pardon, E]] | ||
| + | [[Category: Steyaert, J]] | ||
| + | [[Category: General secretory pathway]] | ||
| + | [[Category: Methylation]] | ||
| + | [[Category: Protein transport-immune system complex]] | ||
| + | [[Category: Pseudopilin]] | ||
| + | [[Category: Single chain antibody]] | ||
Current revision
Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus
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