1sjv: Difference between revisions

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-[[Image:1sjv.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1sjv", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1sjv|  PDB=1sjv  |  SCENE=  }}
-'''Three-Dimensional Structure of a Llama VHH Domain Swapping'''
+==Three-Dimensional Structure of a Llama VHH Domain Swapping==
+<StructureSection load='1sjv' size='340' side='right'caption='[[1sjv]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1sjv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJV FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94&#8491;</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=1sjv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjv OCA], [https://pdbe.org/1sjv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sjv RCSB], [https://www.ebi.ac.uk/pdbsum/1sjv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjv 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/sj/1sjv_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=1sjv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH-R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K(d) value of 83 nM. However, the crystal structure of VHH-R9 exhibits a striking feature: its CDR3 and its last beta-strand (beta9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry-related molecule. The two monomers thus form a domain-swapped dimer which establishes further contacts with symmetry-related molecules and build a crystal-wide beta-sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.
-==Overview==
+Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure.,Spinelli S, Desmyter A, Frenken L, Verrips T, Tegoni M, Cambillau C FEBS Lett. 2004 Apr 23;564(1-2):35-40. PMID:15094039<ref>PMID:15094039</ref>
-Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH-R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K(d) value of 83 nM. However, the crystal structure of VHH-R9 exhibits a striking feature: its CDR3 and its last beta-strand (beta9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry-related molecule. The two monomers thus form a domain-swapped dimer which establishes further contacts with symmetry-related molecules and build a crystal-wide beta-sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-SJV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJV OCA].
+</div>
+<div class="pdbe-citations 1sjv" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure., Spinelli S, Desmyter A, Frenken L, Verrips T, Tegoni M, Cambillau C, FEBS Lett. 2004 Apr 23;564(1-2):35-40. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15094039 15094039]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Lama glama]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Cambillau, C.]]
+[[Category: Cambillau C]]
-[[Category: Desmyter, A.]]
+[[Category: Desmyter A]]
-[[Category: Frenken, L.]]
+[[Category: Frenken L]]
-[[Category: Spinelli, S.]]
+[[Category: Spinelli S]]
-[[Category: Verrips, T.]]
+[[Category: Verrips T]]
-[[Category: Camelids antibody]]
-[[Category: Domain swapping]]
-[[Category: Heavy chain antibody]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:47:47 2008''