3bvn: Difference between revisions

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==High resolution crystal structure of HLA-B*1402 in complex with the latent membrane protein 2 peptide (LMP2) of Epstein-Barr virus==

== Structural highlights ==

<table><tr><td colspan='2'>[[3bvn]] is a 6 chain structure with 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=3BVN OCA]. For a guided tour on the structure components use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BVN FirstGlance].

<table><tr><td colspan='2'>[[3bvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_herpesvirus_4_strain_B95-8 Human herpesvirus 4 strain B95-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVN OCA]. For a guided tour on the structure components use [https://proteopedia.org/fgij/fg.htm?mol=3BVN FirstGlance].

</td></tr><tr id='~~related~~'><td class="sblockLbl">[[~~Related_structure~~|~~Related~~:]]</td><td class="sblockDat"~~>[[1uxs|1uxs]]</td></tr>~~

</td></tr><tr id='method'><td class="sblockLbl">[[Empirical_models|Method:]]</td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55Å</td></tr>

~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~~~[[~~Gene~~|~~Gene:~~]]~~</td><td class="sblockDat">HLA-B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), B2M ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5~~&~~id=9606 Homo sapiens])~~</td></tr>

<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[https://proteopedia.org/fgij/fg.htm?mol=3bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvn OCA], [https://pdbe.org/3bvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvn RCSB], [https://www.ebi.ac.uk/pdbsum/3bvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvn ProSAT]</td></tr>

<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvn OCA], [~~http~~://pdbe.org/3bvn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bvn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bvn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvn ProSAT]</td></tr>

</table>

~~== Disease ==~~

[[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[http://omim.org/entry/241600 241600]]. Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation.<ref>PMID:16549777</ref> Note=Beta-2-microglobulin may adopt the fibrillar configuration of amyloid in certain pathologic states. The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta(2)-microglobulin serum levels lead to amyloidosis in patients on long-term hemodialysis.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>

== Function ==

[~~[http~~://www.uniprot.org/uniprot/~~LMP2_EBVB9 LMP2_EBVB9~~]] Isoform LMP2A maintains EBV latent infection of B-lymphocyte, by preventing lytic reactivation of the virus in response to surface immunoglobulin (sIg) cross-linking. Acts like a dominant negative inhibitor of the sIg-associated protein tyrosine kinases, LYN and SYK. Also blocks translocation of the B-cell antigen receptor (BCR) into lipid rafts, preventing the subsequent signaling and accelerated internalization of the BCR upon BCR cross-linking. Serves as a molecular scaffold to recruit SYK, LYN and E3 protein-ubiquitin ligases, such as ITCH and NEDD4L, leading to ubiquitination and potential degradation of both tyrosines kinases. Possesses a constitutive signaling activity in non-transformed cells, inducing bypass of normal B lymphocyte developmental checkpoints allowing immunoglobulin-negative cells to colonize peripheral lymphoid organs.<ref>PMID:8290598</ref> <ref>PMID:9768760</ref> Isoform LMP2B may be a negative regulator of isoform LMP2A.<ref>PMID:8290598</ref> <ref>PMID:9768760</ref> [[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system.

[https://www.uniprot.org/uniprot/Q56H30_HUMAN Q56H30_HUMAN]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/3bvn_consurf.spt"</scriptWhenChecked>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/3bvn_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>

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==See Also==

*[[Beta-2 microglobulin|Beta-2 microglobulin]]

*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]

*[[~~Major histocompatibility complex~~|~~Major histocompatibility complex~~]]

*[[MHC 3D structures|MHC 3D structures]]

*[[MHC I 3D structures|MHC I 3D structures]]

== References ==

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</StructureSection>

[[Category: Homo sapiens]]

[[Category: ~~Kumar, P]]~~

[[Category: Human herpesvirus 4 strain B95-8]]

~~[[Category: Saenger, W]]~~

[[Category: Large Structures]]

~~[[Category: Uchanska~~-~~Ziegler, B~~]]

[[Category: Kumar P]]

[[Category: ~~Vahedi-Faridi, A~~]]

[[Category: Saenger W]]

[[Category: ~~Ziegler, A~~]]

[[Category: Uchanska-Ziegler B]]

[[Category: ~~Ankylosing spondylitis~~]]

[[Category: Vahedi-Faridi A]]

[[Category: ~~Disease mutation]]~~

[[Category: Ziegler A]]

~~[[Category: Glycation]]~~

~~[[Category: Glycoprotein]]~~

~~[[Category: Hla]]~~

~~[[Category: Hla~~-~~b*14~~]]

[[Category: ~~Hla~~-~~b*1402~~]]

[[Category: ~~Hla-b14]]~~

~~[[Category: Hla-b1402]]~~

~~[[Category: Host-virus interaction]]~~

~~[[Category: Human leukocyte antigen]]~~

~~[[Category: Immune response]]~~

~~[[Category: Immune system]]~~

~~[[Category: Immunoglobulin domain]]~~

~~[[Category: Major histocompatibility complex]]~~

~~[[Category: Membrane]]~~

~~[[Category: Mhc]]~~

~~[[Category: Mhc i]]~~

~~[[Category: Phosphoprotein]]~~

~~[[Category: Plmp2]]~~

~~[[Category: Pyrrolidone carboxylic acid]]~~

~~[[Category: Secreted]]~~

~~[[Category: Transmembrane~~]]

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@@ Line 1: / Line 1: @@
 ==High resolution crystal structure of HLA-B*1402 in complex with the latent membrane protein 2 peptide (LMP2) of Epstein-Barr virus==
-<StructureSection load='3bvn' size='340' side='right' caption='[[3bvn]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+<StructureSection load='3bvn' size='340' side='right'caption='[[3bvn]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bvn]] is a 6 chain structure with 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=3BVN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BVN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bvn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_herpesvirus_4_strain_B95-8 Human herpesvirus 4 strain B95-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BVN FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uxs|1uxs]]</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]] 2.55&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HLA-B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), B2M ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvn OCA], [https://pdbe.org/3bvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvn RCSB], [https://www.ebi.ac.uk/pdbsum/3bvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvn ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvn OCA], [http://pdbe.org/3bvn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bvn RCSB], [http://www.ebi.ac.uk/pdbsum/3bvn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvn ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[http://omim.org/entry/241600 241600]]. Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation.<ref>PMID:16549777</ref>   Note=Beta-2-microglobulin may adopt the fibrillar configuration of amyloid in certain pathologic states. The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta(2)-microglobulin serum levels lead to amyloidosis in patients on long-term hemodialysis.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/LMP2_EBVB9 LMP2_EBVB9]] Isoform LMP2A maintains EBV latent infection of B-lymphocyte, by preventing lytic reactivation of the virus in response to surface immunoglobulin (sIg) cross-linking. Acts like a dominant negative inhibitor of the sIg-associated protein tyrosine kinases, LYN and SYK. Also blocks translocation of the B-cell antigen receptor (BCR) into lipid rafts, preventing the subsequent signaling and accelerated internalization of the BCR upon BCR cross-linking. Serves as a molecular scaffold to recruit SYK, LYN and E3 protein-ubiquitin ligases, such as ITCH and NEDD4L, leading to ubiquitination and potential degradation of both tyrosines kinases. Possesses a constitutive signaling activity in non-transformed cells, inducing bypass of normal B lymphocyte developmental checkpoints allowing immunoglobulin-negative cells to colonize peripheral lymphoid organs.<ref>PMID:8290598</ref> <ref>PMID:9768760</ref>   Isoform LMP2B may be a negative regulator of isoform LMP2A.<ref>PMID:8290598</ref> <ref>PMID:9768760</ref>  [[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system.
+[https://www.uniprot.org/uniprot/Q56H30_HUMAN Q56H30_HUMAN]
 == 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/bv/3bvn_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/3bvn_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 33: / Line 30: @@
 ==See Also==
-*[[Beta-2 microglobulin|Beta-2 microglobulin]]
+*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
-*[[Major histocompatibility complex|Major histocompatibility complex]]
+*[[MHC 3D structures|MHC 3D structures]]
+*[[MHC I 3D structures|MHC I 3D structures]]
 == References ==
 <references/>
@@ Line 40: / Line 38: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Kumar, P]]
+[[Category: Human herpesvirus 4 strain B95-8]]
-[[Category: Saenger, W]]
+[[Category: Large Structures]]
-[[Category: Uchanska-Ziegler, B]]
+[[Category: Kumar P]]
-[[Category: Vahedi-Faridi, A]]
+[[Category: Saenger W]]
-[[Category: Ziegler, A]]
+[[Category: Uchanska-Ziegler B]]
-[[Category: Ankylosing spondylitis]]
+[[Category: Vahedi-Faridi A]]
-[[Category: Disease mutation]]
+[[Category: Ziegler A]]
-[[Category: Glycation]]
-[[Category: Glycoprotein]]
-[[Category: Hla]]
-[[Category: Hla-b*14]]
-[[Category: Hla-b*1402]]
-[[Category: Hla-b14]]
-[[Category: Hla-b1402]]
-[[Category: Host-virus interaction]]
-[[Category: Human leukocyte antigen]]
-[[Category: Immune response]]
-[[Category: Immune system]]
-[[Category: Immunoglobulin domain]]
-[[Category: Major histocompatibility complex]]
-[[Category: Membrane]]
-[[Category: Mhc]]
-[[Category: Mhc i]]
-[[Category: Phosphoprotein]]
-[[Category: Plmp2]]
-[[Category: Pyrrolidone carboxylic acid]]
-[[Category: Secreted]]
-[[Category: Transmembrane]]