3bj9: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3bj9.png|left|200px]]
-<!--
+==Crystal structure of the Surrogate Light Chain Variable Domain VpreBJ==
-The line below this paragraph, containing "STRUCTURE_3bj9", creates the "Structure Box" on the page.
+<StructureSection load='3bj9' size='340' side='right'caption='[[3bj9]], [[Resolution|resolution]] 2.00&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'>[[3bj9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJ9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
--->
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VPREB1, VPREB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-{{STRUCTURE_3bj9|  PDB=3bj9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bj9 OCA], [https://pdbe.org/3bj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bj9 RCSB], [https://www.ebi.ac.uk/pdbsum/3bj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bj9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/VPREB_HUMAN VPREB_HUMAN]] Associates with the Ig-mu chain to form a molecular complex that is expressed on the surface of pre-B-cells. This complex presumably regulates Ig gene rearrangements in the early steps of B-cell differentiation.
+== 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/bj/3bj9_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=3bj9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The surrogate light chain (SLC) is a key regulator of B cell development in the bone marrow, resulting in mature B cells that produce antibodies that are capable of interacting with antigens. The SLC comprises two noncovalently interacting proteins: VpreB and 14.1. We engineered a construct to represent the complete immunoglobulin-like domain of the SLC variable domain in a single protein chain that could be bacterially expressed. In this construct, the incomplete immunoglobulin domain of VpreB (residues 1-102) was linked to the J-segment of 14.1 (residues 40-53), which provided one beta-strand to complete the V-like domain (VpreBJ). Because VpreBJ has the interface to VH chains, but lacks the unique region of 14.1, which is important for SLC signaling, we predict that a properly folded VpreBJ would have the potential to act as a dominant negative mutant of the surrogate light chain. X-ray crystallography of VpreBJ at 2.0 A resolution showed that the engineering was successful. With its two beta-pleated sheets, packed face-to-face, the single chain VpreBJ resembles a mature light chain immunoglobulin V-domain (VL). The surface that would normally interact with the VH chain interacts with a crystallographically related VpreBJ molecule. The presence of dimeric species in solution was verified by analytical ultracentrifugation. VpreBJ is easily overexpressed in bacteria, while retaining the native conformation of an immunoglobulin domain, and thus may serve as an important reagent for future studies in B-cell development.
-===Crystal structure of the Surrogate Light Chain Variable Domain VpreBJ===
+Engineering and characterization of a single chain surrogate light chain variable domain.,Morstadt L, Bohm A, Yuksel D, Kumar K, Stollar BD, Baleja JD Protein Sci. 2008 Mar;17(3):458-65. PMID:18287279<ref>PMID:18287279</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18287279}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3bj9" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18287279 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18287279}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Human]]
-BJ9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJ9 OCA].
+[[Category: Large Structures]]
+[[Category: Baleja, J D]]
-==Reference==
+[[Category: Bohm, A A]]
-Engineering and characterization of a single chain surrogate light chain variable domain., Morstadt L, Bohm A, Yuksel D, Kumar K, Stollar BD, Baleja JD, Protein Sci. 2008 Mar;17(3):458-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18287279 18287279]
+[[Category: Morstadt, L M]]
-[[Category: Homo sapiens]]
+[[Category: Stollar, B D]]
-[[Category: Single protein]]
-[[Category: Baleja, J D.]]
-[[Category: Bohm, A A.]]
-[[Category: Morstadt, L M.]]
-[[Category: Stollar, B D.]]
 [[Category: Beta sheet]]
 [[Category: Immune system]]
 [[Category: Immunoglobulin domain]]
 [[Category: Polymorphism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:38:51 2008''