2pkd: Difference between revisions

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New page: left|200px<br /> <applet load="2pkd" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pkd, resolution 2.043Å" /> '''Crystal structure ...
 
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[[Image:2pkd.gif|left|200px]]<br />
<applet load="2pkd" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2pkd, resolution 2.043&Aring;" />
'''Crystal structure of CD84: Insite into SLAM family function'''<br />


==Overview==
==Crystal structure of CD84: Insite into SLAM family function==
The signaling lymphocyte activation molecule (SLAM) family includes, homophilic and heterophilic receptors that modulate both adaptive and, innate immune responses. These receptors share a common ectodomain, organization: a membrane-proximal immunoglobulin constant domain and a, membrane-distal immunoglobulin variable domain that is responsible for, ligand recognition. CD84 is a homophilic family member that enhances, IFN-gamma secretion in activated T cells. Our solution studies revealed, that CD84 strongly self-associates with a K(d) in the submicromolar range., These data, in combination with previous reports, demonstrate that the, SLAM family homophilic affinities span at least three orders of magnitude, and suggest that differences in the affinities may contribute to the, distinct signaling behavior exhibited by the individual family members., The 2.0 A crystal structure of the human CD84 immunoglobulin variable, domain revealed an orthogonal homophilic dimer with high similarity to the, recently reported homophilic dimer of the SLAM family member NTB-A., Structural and chemical differences in the homophilic interfaces provide a, mechanism to prevent the formation of undesired heterodimers among the, SLAM family homophilic receptors. These structural data also suggest that, like NTB-A, all SLAM family homophilic dimers adopt a highly kinked, organization spanning an end-to-end distance of approximately 140 A. This, common molecular dimension provides an opportunity for all two-domain SLAM, family receptors to colocalize within the immunological synapse and bridge, the T cell and antigen-presenting cell.
<StructureSection load='2pkd' size='340' side='right'caption='[[2pkd]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2pkd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKD FirstGlance]. <br>
2PKD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with CL as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PKD OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.043&#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>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pkd OCA], [https://pdbe.org/2pkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pkd RCSB], [https://www.ebi.ac.uk/pdbsum/2pkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pkd ProSAT]</span></td></tr>
Structure of CD84 provides insight into SLAM family function., Yan Q, Malashkevich VN, Fedorov A, Fedorov E, Cao E, Lary JW, Cole JL, Nathenson SG, Almo SC, Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10583-8. Epub 2007 Jun 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17563375 17563375]
</table>
== Function ==
[https://www.uniprot.org/uniprot/SLAF5_HUMAN SLAF5_HUMAN] Plays a role as adhesion receptor functioning by homophilic interactions and by clustering. Recruits SH2 domain-containing proteins SH2D1A/SAP. Increases proliferative responses of activated T-cells and SH2D1A/SAP does not seen be required for this process. Homophilic interactions enhance interferon gamma/IFNG secretion in lymphocytes and induce platelet stimulation via a SH2D1A/SAP-dependent pathway. May serve as a marker for hematopoietic progenitor cells.<ref>PMID:11564780</ref> <ref>PMID:12115647</ref> <ref>PMID:12928397</ref> <ref>PMID:12962726</ref> <ref>PMID:16037392</ref>
== 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/pk/2pkd_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=2pkd ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Almo, S.C.]]
[[Category: Almo SC]]
[[Category: Cao, E.]]
[[Category: Cao E]]
[[Category: Cole, J.L.]]
[[Category: Cole JL]]
[[Category: Fedorov, A.]]
[[Category: Fedorov A]]
[[Category: Lary, J.W.]]
[[Category: Lary JW]]
[[Category: Malashkevich, V.N.]]
[[Category: Malashkevich VN]]
[[Category: Nathenson, S.G.]]
[[Category: Nathenson SG]]
[[Category: Yan, Q.]]
[[Category: Yan Q]]
[[Category: CL]]
[[Category: igc]]
[[Category: igv]]
[[Category: immunoglobulin constant]]
[[Category: immunoglobulin variable]]
[[Category: signaling lymphocyte activation molecule]]
[[Category: slam]]
 
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Retrieved from "https://proteopedia.org/2pkd"