1t1w

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[[Image:1t1w.gif|left|200px]]
 
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==Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3F6I8V==
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The line below this paragraph, containing "STRUCTURE_1t1w", creates the "Structure Box" on the page.
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<StructureSection load='1t1w' size='340' side='right'caption='[[1t1w]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1t1w]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T1W FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t1w OCA], [https://pdbe.org/1t1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t1w RCSB], [https://www.ebi.ac.uk/pdbsum/1t1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t1w ProSAT]</span></td></tr>
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{{STRUCTURE_1t1w| PDB=1t1w | SCENE= }}
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</table>
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== Disease ==
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'''Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3F6I8V'''
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[https://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[https://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>
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== Function ==
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[https://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.
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==Overview==
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t1/1t1w_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1t1w ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
It is well established that even small changes in amino acid side chains of antigenic peptide bound to major histocompatibility complex (MHC) protein may completely abrogate recognition of the peptide-MHC (pMHC) complex by the T cell receptor (TCR). Often, however, several nonconservative substitutions in the peptide antigen are accommodated and do not impair its recognition by TCR. For example, a preponderance of natural sequence variants of the human immunodeficiency virus p17 Gag-derived peptide SLYNTVATL (SL9) are recognized by cytotoxic T lymphocytes, which implies that interactions with SL9 variants are degenerate both with respect to the class I MHC molecule and with respect to TCR. Here we study the molecular basis for this degenerate recognition of SL9 variants. We show that several SL9 variants bind comparably well to soluble HLA-A2 and to a particular soluble TCR and that these variants are active in the cognate cytotoxicity assay. Natural SL9 variation is restricted by its context in the HIV p17 matrix protein. High resolution crystal structures of seven selected SL9 variants bound to HLA-A2 all have remarkably similar peptide conformations and side-chain dispositions outside sites of substitution. This preservation of the peptide conformation despite epitope variations suggests a mechanism for the observed degeneracy in pMHC recognition by TCR and may contribute to the persistence of SL9-mediated immune responses in chronically infected individuals.
It is well established that even small changes in amino acid side chains of antigenic peptide bound to major histocompatibility complex (MHC) protein may completely abrogate recognition of the peptide-MHC (pMHC) complex by the T cell receptor (TCR). Often, however, several nonconservative substitutions in the peptide antigen are accommodated and do not impair its recognition by TCR. For example, a preponderance of natural sequence variants of the human immunodeficiency virus p17 Gag-derived peptide SLYNTVATL (SL9) are recognized by cytotoxic T lymphocytes, which implies that interactions with SL9 variants are degenerate both with respect to the class I MHC molecule and with respect to TCR. Here we study the molecular basis for this degenerate recognition of SL9 variants. We show that several SL9 variants bind comparably well to soluble HLA-A2 and to a particular soluble TCR and that these variants are active in the cognate cytotoxicity assay. Natural SL9 variation is restricted by its context in the HIV p17 matrix protein. High resolution crystal structures of seven selected SL9 variants bound to HLA-A2 all have remarkably similar peptide conformations and side-chain dispositions outside sites of substitution. This preservation of the peptide conformation despite epitope variations suggests a mechanism for the observed degeneracy in pMHC recognition by TCR and may contribute to the persistence of SL9-mediated immune responses in chronically infected individuals.
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==Disease==
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Structural basis for degenerate recognition of natural HIV peptide variants by cytotoxic lymphocytes.,Martinez-Hackert E, Anikeeva N, Kalams SA, Walker BD, Hendrickson WA, Sykulev Y J Biol Chem. 2006 Jul 21;281(29):20205-12. Epub 2006 May 15. PMID:16702212<ref>PMID:16702212</ref>
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Known disease associated with this structure: Hypoproteinemia, hypercatabolic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=109700 109700]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1T1W is a [[Protein complex]] structure of sequences 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=1T1W OCA].
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</div>
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<div class="pdbe-citations 1t1w" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Structural basis for degenerate recognition of natural HIV peptide variants by cytotoxic lymphocytes., Martinez-Hackert E, Anikeeva N, Kalams SA, Walker BD, Hendrickson WA, Sykulev Y, J Biol Chem. 2006 Jul 21;281(29):20205-12. Epub 2006 May 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16702212 16702212]
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*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
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*[[MHC 3D structures|MHC 3D structures]]
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*[[MHC I 3D structures|MHC I 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Protein complex]]
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[[Category: Human immunodeficiency virus 1]]
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[[Category: Anikeeva, N.]]
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[[Category: Large Structures]]
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[[Category: Hendrickson, W A.]]
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[[Category: Anikeeva N]]
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[[Category: Kalams, S A.]]
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[[Category: Hendrickson WA]]
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[[Category: Martinez-Hackert, E.]]
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[[Category: Kalams SA]]
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[[Category: Sykulev, Y.]]
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[[Category: Martinez-Hackert E]]
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[[Category: Walker, B D.]]
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[[Category: Sykulev Y]]
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[[Category: Ctl]]
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[[Category: Walker BD]]
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[[Category: Cytotoxic t lymphocyte]]
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[[Category: Hiv]]
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[[Category: Human immunodeficiency virus]]
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[[Category: Major histocompatibility complex]]
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[[Category: Mhc]]
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[[Category: Peptide mhc complex]]
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[[Category: Pmhc]]
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[[Category: Rmsd]]
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[[Category: Root-mean-squared deviation]]
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[[Category: Simian immunodeficiency virus]]
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[[Category: Siv]]
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[[Category: T-cell receptor]]
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[[Category: Tcr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:24:16 2008''
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Current revision

Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-3F6I8V

PDB ID 1t1w

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