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.


2yxf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /> <applet load="2yxf" size="450" color="white" frame="true" align="right" spinBox="true" caption="2yxf, resolution 1.13&Aring;" /> '''The high resolution...)
Current revision (09:09, 25 October 2023) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2yxf.gif|left|200px]]<br />
 
-
<applet load="2yxf" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2yxf, resolution 1.13&Aring;" />
 
-
'''The high resolution crystal structure of beta2-microglobulin under physiological conditions'''<br />
 
-
==Overview==
+
==The high resolution crystal structure of beta2-microglobulin under physiological conditions==
-
beta(2)-Microglobulin (beta2-m), a light chain of the major, histocompatibility complex class I, forms amyloid fibrils in patients, undergoing long-term haemodialysis, causing dialysis-related amyloidosis., Based on a comparison of the X-ray structure obtained at pH 5.7 and that, of beta2-m in the histocompatibility complex, it has been proposed that, the continuous D-strand observed in the crystal structure at pH 5.7, increases the propensity of beta2-m to self-associate via edge-to-edge, interactions, thus initiating the formation of fibrils. To obtain further, insight into the mechanism by which amyloid fibrils form, we determined, the crystal structure of beta2-m at pH 7.0 at a resolution of up to 1.13, A. The crystal structure at pH 7.0 was basically the same as that at pH, 5.6, suggesting that the conversion of the beta-bulge in strand D into a, contiguous beta-strand is not unique to the crystals formed under slightly, acidic conditions. In other words, although the formation of beta2-m, fibrils was enhanced under acidic conditions, it remains unknown if it is, related to the increased propensity for the disappearance of the, beta-bulge in strand D. We consider that the enhanced fibrillation is more, directly coupled with the decreased stability leading to the increased, propensity of exposing amyloidogenic regions.
+
<StructureSection load='2yxf' size='340' side='right'caption='[[2yxf]], [[Resolution|resolution]] 1.13&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2yxf]] is a 1 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=2YXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YXF FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.13&#8491;</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=2yxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxf OCA], [https://pdbe.org/2yxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yxf RCSB], [https://www.ebi.ac.uk/pdbsum/2yxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yxf ProSAT]</span></td></tr>
 +
</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 ==
 +
[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.
 +
== 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/yx/2yxf_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=2yxf ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
beta(2)-Microglobulin (beta2-m), a light chain of the major histocompatibility complex class I, forms amyloid fibrils in patients undergoing long-term haemodialysis, causing dialysis-related amyloidosis. Based on a comparison of the X-ray structure obtained at pH 5.7 and that of beta2-m in the histocompatibility complex, it has been proposed that the continuous D-strand observed in the crystal structure at pH 5.7 increases the propensity of beta2-m to self-associate via edge-to-edge interactions, thus initiating the formation of fibrils. To obtain further insight into the mechanism by which amyloid fibrils form, we determined the crystal structure of beta2-m at pH 7.0 at a resolution of up to 1.13 A. The crystal structure at pH 7.0 was basically the same as that at pH 5.6, suggesting that the conversion of the beta-bulge in strand D into a contiguous beta-strand is not unique to the crystals formed under slightly acidic conditions. In other words, although the formation of beta2-m fibrils was enhanced under acidic conditions, it remains unknown if it is related to the increased propensity for the disappearance of the beta-bulge in strand D. We consider that the enhanced fibrillation is more directly coupled with the decreased stability leading to the increased propensity of exposing amyloidogenic regions.
-
==Disease==
+
High-resolution crystal structure of beta2-microglobulin formed at pH 7.0.,Iwata K, Matsuura T, Sakurai K, Nakagawa A, Goto Y J Biochem. 2007 Sep;142(3):413-9. Epub 2007 Jul 23. PMID:17646174<ref>PMID:17646174</ref>
-
Known disease associated with this structure: Hypoproteinemia, hypercatabolic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=109700 109700]]
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
2YXF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2YXF OCA].
+
</div>
 +
<div class="pdbe-citations 2yxf" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
High-resolution Crystal Structure of {beta}2-Microglobulin Formed at pH 7.0., Iwata K, Matsuura T, Sakurai K, Nakagawa A, Goto Y, J Biochem (Tokyo). 2007 Sep;142(3):413-9. Epub 2007 Jul 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17646174 17646174]
+
*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Goto, Y.]]
+
[[Category: Goto Y]]
-
[[Category: Iwata, K.]]
+
[[Category: Iwata K]]
-
[[Category: Matsuura, T.]]
+
[[Category: Matsuura T]]
-
[[Category: Nakagawa, A.]]
+
[[Category: Nakagawa A]]
-
[[Category: immune system]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:46:22 2007''
+

Current revision

The high resolution crystal structure of beta2-microglobulin under physiological conditions

PDB ID 2yxf

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/2yxf"
Personal tools