3cfi: Difference between revisions

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-{{Seed}}
-[[Image:3cfi.jpg|left|200px]]
-<!--
+==Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus==
-The line below this paragraph, containing "STRUCTURE_3cfi", creates the "Structure Box" on the page.
+<StructureSection load='3cfi' size='340' side='right'caption='[[3cfi]], [[Resolution|resolution]] 2.58&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3cfi]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. 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>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.58&#8491;</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>
-{{STRUCTURE_3cfi|  PDB=3cfi  |  SCENE=  }}
+<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>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7MPZ1_VIBVY Q7MPZ1_VIBVY]
+== 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/initialview03.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 heterdimer from Vibrio Vulnificus===
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3cfi" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19118632}}, adds the Publication Abstract to the page
+*[[Pseudopilin|Pseudopilin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19118632 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19118632}}
+__TOC__
+</StructureSection>
-==About this Structure==
-CFI is a 12 chains structure of sequences from [http://en.wikipedia.org/wiki/Lama_glama Lama glama] and [http://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CFI OCA].
-==Reference==
-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. 2008 Dec 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19118632 19118632]
 [[Category: Lama glama]]
+[[Category: Large Structures]]
 [[Category: Vibrio vulnificus]]
-[[Category: Hol, W G.J.]]
+[[Category: Hol WGJ]]
-[[Category: Korotkov, K V.]]
+[[Category: Korotkov KV]]
-[[Category: Lam, A Y.]]
+[[Category: Lam AY]]
-[[Category: Pardon, E.]]
+[[Category: Pardon E]]
-[[Category: Steyaert, J.]]
+[[Category: Steyaert J]]
-[[Category: General secretory pathway]]
-[[Category: Methylation]]
-[[Category: Protein transport/immune system complex]]
-[[Category: Pseudopilin]]
-[[Category: Single chain antibody]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 13:09:14 2009''