3cfi

From Proteopedia

(Difference between revisions)

Current revision

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

Structural highlights

3cfi is a 12 chain structure with sequence from Lama glama and Vibrio vulnificus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.58Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q7MPZ1_VIBVY

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lam AY, Pardon E, Korotkov KV, Hol WG, Steyaert J. Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus. J Struct Biol. 2009 Apr;166(1):8-15. Epub 2008 Dec 10. PMID:19118632 doi:10.1016/j.jsb.2008.11.008

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3cfi"

@@ Line 3: / Line 3: @@
 <StructureSection load='3cfi' size='340' side='right'caption='[[3cfi]], [[Resolution|resolution]] 2.58&Aring;' 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>
+<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>
-</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>
+</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='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='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='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]]
@@ Line 13: / Line 15: @@
   <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>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 27562]]
+[[Category: Lama glama]]
-[[Category: Camelus glama]]
 [[Category: Large Structures]]
-[[Category: Hol, W G.J]]
+[[Category: Vibrio vulnificus]]
-[[Category: Korotkov, K V]]
+[[Category: Hol WGJ]]
-[[Category: Lam, A Y]]
+[[Category: Korotkov KV]]
-[[Category: Pardon, E]]
+[[Category: Lam AY]]
-[[Category: Steyaert, J]]
+[[Category: Pardon E]]
-[[Category: General secretory pathway]]
+[[Category: Steyaert J]]
-[[Category: Methylation]]
-[[Category: Protein transport-immune system complex]]
-[[Category: Pseudopilin]]
-[[Category: Single chain antibody]]

3cfi

From Proteopedia

Current revision

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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