5xp1

From Proteopedia

(Difference between revisions)

Current revision

Structure of monomeric mutant of REI immunoglobulin light chain variable domain crystallized at pH 6

Structural highlights

5xp1 is a 8 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.88Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KVD33_HUMAN V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:20176268, PubMed:17576170).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Amyloid light-chain (AL) amyloidosis is a protein-misfolding disease characterized by accumulation of immunoglobulin light chains (LCs) into amyloid fibrils. Dimerization of a full length or variable domain (VL ) of LC serves to stabilize the native state and prevent the formation of amyloid fibrils. We here analyzed the thermodynamic properties of dimerization and unfolding reactions by nonamyloidogenic VL from REI LC or its monomeric Y96K mutant using sedimentation velocity and circular dichroism. The data indicate that the equilibrium shifts to native dimerization for wild-type REI VL by elevating temperature due to the negative enthalpy change for dimer dissociation (-81.2 kJ.mol-1 ). The Y96K mutation did not affect the stability of the monomeric native state but increased amyloidogenicity. These results suggest that the heat-induced native homodimerization is the major factor preventing amyloid formation by wild-type REI VL . Heat-induced native oligomerization may be an efficient strategy to avoid the formation of misfolded aggregates particularly for thermostable proteins that are used at elevated temperatures under conditions where other proteins tend to misfold. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 5XP1 and 5XQY.

Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI.,Nawata M, Tsutsumi H, Kobayashi Y, Unzai S, Mine S, Nakamura T, Uegaki K, Kamikubo H, Kataoka M, Hamada D FEBS J. 2017 Sep;284(18):3114-3127. doi: 10.1111/febs.14181. Epub 2017 Aug 13. PMID:28736891^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20. PMID:17576170 doi:http://dx.doi.org/10.1146/annurev.genet.41.110306.130340
↑ Schroeder HW Jr, Cavacini L. Structure and function of immunoglobulins. J Allergy Clin Immunol. 2010 Feb;125(2 Suppl 2):S41-52. doi:, 10.1016/j.jaci.2009.09.046. PMID:20176268 doi:http://dx.doi.org/10.1016/j.jaci.2009.09.046
↑ McHeyzer-Williams M, Okitsu S, Wang N, McHeyzer-Williams L. Molecular programming of B cell memory. Nat Rev Immunol. 2011 Dec 9;12(1):24-34. doi: 10.1038/nri3128. PMID:22158414 doi:http://dx.doi.org/10.1038/nri3128
↑ Lefranc MP. Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics. Front Immunol. 2014 Feb 5;5:22. doi: 10.3389/fimmu.2014.00022. eCollection 2014. PMID:24600447 doi:http://dx.doi.org/10.3389/fimmu.2014.00022
↑ Nawata M, Tsutsumi H, Kobayashi Y, Unzai S, Mine S, Nakamura T, Uegaki K, Kamikubo H, Kataoka M, Hamada D. Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI. FEBS J. 2017 Sep;284(18):3114-3127. doi: 10.1111/febs.14181. Epub 2017 Aug 13. PMID:28736891 doi:http://dx.doi.org/10.1111/febs.14181

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5xp1"

@@ Line 3: / Line 3: @@
 <StructureSection load='5xp1' size='340' side='right'caption='[[5xp1]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xp1]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5b3c 5b3c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XP1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xp1]] is a 8 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=5XP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XP1 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]] 2.88&#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=5xp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xp1 OCA], [https://pdbe.org/5xp1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xp1 RCSB], [https://www.ebi.ac.uk/pdbsum/5xp1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xp1 ProSAT]</span></td></tr>

5xp1

From Proteopedia

Current revision

Structure of monomeric mutant of REI immunoglobulin light chain variable domain crystallized at pH 6

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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