2i25

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme

Structural highlights

2i25 is a 4 chain structure with sequence from Gallus gallus and Ginglymostoma cirratum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8AXH5_GINCI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

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

References

↑ Stanfield RL, Dooley H, Verdino P, Flajnik MF, Wilson IA. Maturation of shark single-domain (IgNAR) antibodies: evidence for induced-fit binding. J Mol Biol. 2007 Mar 23;367(2):358-72. Epub 2006 Dec 22. PMID:17258766 doi:10.1016/j.jmb.2006.12.045

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2i25"

Categories: Gallus gallus | Ginglymostoma cirratum | Large Structures | Stanfield RL | Wilson IA

@@ Line 3: / Line 3: @@
 <StructureSection load='2i25' size='340' side='right'caption='[[2i25]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2i25]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ginci Ginci] and [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I25 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2I25 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2i25]] is a 4 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=2I25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I25 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2i24|2i24]], [[2i26|2i26]], [[2i27|2i27]]</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]] 1.8&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=2i25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i25 OCA], [https://pdbe.org/2i25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i25 RCSB], [https://www.ebi.ac.uk/pdbsum/2i25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i25 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2i25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i25 OCA], [http://pdbe.org/2i25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i25 RCSB], [http://www.ebi.ac.uk/pdbsum/2i25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i25 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
+[https://www.uniprot.org/uniprot/Q8AXH5_GINCI Q8AXH5_GINCI]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i2/2i25_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 37: / Line 36: @@
 </StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Ginci]]
+[[Category: Ginglymostoma cirratum]]
 [[Category: Large Structures]]
-[[Category: Lysozyme]]
+[[Category: Stanfield RL]]
-[[Category: Stanfield, R L]]
+[[Category: Wilson IA]]
-[[Category: Wilson, I A]]
-[[Category: Immune system]]
-[[Category: Immunoglobulin fold]]
-[[Category: Protein-protein complex]]

2i25

From Proteopedia

Current revision

Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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