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[[Image:2i26.jpg|left|200px]]
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{{STRUCTURE_2i26|  PDB=2i26  |  SCENE=  }}
'''Crystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme'''


==Crystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme==
<StructureSection load='2i26' size='340' side='right'caption='[[2i26]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2i26]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Ginglymostoma_cirratum Ginglymostoma cirratum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I26 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]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2i26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i26 OCA], [https://pdbe.org/2i26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i26 RCSB], [https://www.ebi.ac.uk/pdbsum/2i26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i26 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8JGG7_GINCI Q8JGG7_GINCI]
== 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/i2/2i26_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2i26 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Sharks express an unusual heavy-chain isotype called IgNAR, whose variable regions bind antigen as independent soluble domains. To further probe affinity maturation of the IgNAR response, we structurally characterized the germline and somatically matured versions of a type II variable (V) region, both in the presence and absence of its antigen, hen egg-white lysozyme. Despite a disulfide bond linking complementarity determining regions (CDRs) 1 and 3, both germline and somatically matured V regions displayed significant structural changes in these CDRs upon complex formation with antigen. Somatic mutations in the IgNAR V region serve to increase the number of contacts with antigen, as reflected by a tenfold increase in affinity, and one of these mutations appears to stabilize the CDR3 region. In addition, a residue in the HV4 loop plays an important role in antibody-antigen interaction, consistent with the high rate of somatic mutations in this non-CDR loop.


==Overview==
Maturation of shark single-domain (IgNAR) antibodies: evidence for induced-fit binding.,Stanfield RL, Dooley H, Verdino P, Flajnik MF, Wilson IA J Mol Biol. 2007 Mar 23;367(2):358-72. Epub 2006 Dec 22. PMID:17258766<ref>PMID:17258766</ref>
Sharks express an unusual heavy-chain isotype called IgNAR, whose variable regions bind antigen as independent soluble domains. To further probe affinity maturation of the IgNAR response, we structurally characterized the germline and somatically matured versions of a type II variable (V) region, both in the presence and absence of its antigen, hen egg-white lysozyme. Despite a disulfide bond linking complementarity determining regions (CDRs) 1 and 3, both germline and somatically matured V regions displayed significant structural changes in these CDRs upon complex formation with antigen. Somatic mutations in the IgNAR V region serve to increase the number of contacts with antigen, as reflected by a tenfold increase in affinity, and one of these mutations appears to stabilize the CDR3 region. In addition, a residue in the HV4 loop plays an important role in antibody-antigen interaction, consistent with the high rate of somatic mutations in this non-CDR loop.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2I26 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Ginglymostoma_cirratum Ginglymostoma cirratum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I26 OCA].
</div>
<div class="pdbe-citations 2i26" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Maturation of shark single-domain (IgNAR) antibodies: evidence for induced-fit binding., Stanfield RL, Dooley H, Verdino P, Flajnik MF, Wilson IA, J Mol Biol. 2007 Mar 23;367(2):358-72. Epub 2006 Dec 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17258766 17258766]
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
[[Category: Ginglymostoma cirratum]]
[[Category: Ginglymostoma cirratum]]
[[Category: Lysozyme]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Stanfield RL]]
[[Category: Stanfield, R L.]]
[[Category: Wilson IA]]
[[Category: Wilson, I A.]]
[[Category: Immunoglobulin fold]]
[[Category: Protein-protein complex]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:59:19 2008''

Latest revision as of 08:10, 30 October 2024

Crystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme

2i26, resolution 2.50Å

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