This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3vfm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:27, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3vfm' size='340' side='right'caption='[[3vfm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3vfm' size='340' side='right'caption='[[3vfm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3vfm]] is a 3 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=3VFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3vfm]] is a 3 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=3VFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFM FirstGlance]. <br>
-
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zhk|1zhk]], [[1zhl|1zhl]], [[2ak4|2ak4]], [[3vfn|3vfn]], [[3vfo|3vfo]], [[3vfp|3vfp]], [[3vfr|3vfr]], [[3vfs|3vfs]], [[3vft|3vft]], [[3vfu|3vfu]], [[3vfv|3vfv]], [[3vfw|3vfw]]</div></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]] 1.9&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HLA-B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), B2M, CDABP0092, HDCMA22P ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3vfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfm OCA], [https://pdbe.org/3vfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfm RCSB], [https://www.ebi.ac.uk/pdbsum/3vfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfm ProSAT]</span></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=3vfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfm OCA], [https://pdbe.org/3vfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfm RCSB], [https://www.ebi.ac.uk/pdbsum/3vfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfm ProSAT]</span></td></tr>
</table>
</table>
-
== Disease ==
 
-
[[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>
 
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/C5MK56_HUMAN C5MK56_HUMAN]] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364] [[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.
+
[https://www.uniprot.org/uniprot/C5MK56_HUMAN C5MK56_HUMAN] Involved in the presentation of foreign antigens to the immune system (By similarity).[SAAS:SAAS003006_004_004364]
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
While the Major Histocompatibility Complex Class I (MHC-I) molecules typically bind short peptide (p) fragments (8-10 amino acids in length), longer, bulged, peptides are often be presented by MHC-I. Such bulged pMHC-I complexes represent challenges for T-cell receptor (TCR) ligation, although the general principles underscoring the interaction between TCRs and bulged pMHC-I complexes are unclear. To address this, we have explored the energetic basis of how an immunodominant TCR (termed SB27) binds to a 13 amino acid viral peptide (LPEPLPQGQLTAY) complexed to Human Leukocyte Antigen (HLA) B*3508. Using the crystal structure of the SB27 TCR-HLA B*3508LPEP complex as a guide, we undertook a comprehensive alanine-scanning mutagenesis approach at the TCR-pMHC-I interface and examined the effect of the mutations by biophysical (affinity measurements) and cellular approaches (tetramer staining). While the structural footprint on the HLA B*3508 was small, the energetic footprint was even smaller in that only two HLA B*3508 residues were critical for the TCR interaction. Instead, the energetic basis of this TCR-pMHC-I interaction was attributed to peptide-mediated interactions in which the complementarity determining region (CDR) 3alpha and germline encoded CDR1beta loops of the SB27 TCR played the principal role. Our findings highlight the peptide-centricity of TCR ligation towards a bulged pMHC-I complex.
+
-
 
+
-
The energetic basis underpinning T-cell teceptor tecognition of a super-bulged peptide bound to a major histocompatibility complex class I molecule.,Liu YC, Chen Z, Burrows SR, Purcell AW, McCluskey J, Rossjohn J, Gras S J Biol Chem. 2012 Feb 16. PMID:22343629<ref>PMID:22343629</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3vfm" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
-
== References ==
+
*[[MHC 3D structures|MHC 3D structures]]
-
<references/>
+
*[[MHC I 3D structures|MHC I 3D structures]]
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Gras, S]]
+
[[Category: Gras S]]
-
[[Category: Liu, Y C]]
+
[[Category: Liu YC]]
-
[[Category: Rossjohn, J]]
+
[[Category: Rossjohn J]]
-
[[Category: Antigen-presenting molecule]]
+
-
[[Category: Epstein barr virus]]
+
-
[[Category: Hla b*3508]]
+
-
[[Category: Immune system]]
+
-
[[Category: T cell]]
+
-
[[Category: Tcr]]
+

Current revision

crystal structure of HLA B*3508 LPEP155A, HLA mutant Ala155

PDB ID 3vfm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3vfm"
Personal tools