2d03: Difference between revisions

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-[[Image:2d03.gif|left|200px]]<br />
-<applet load="2d03" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2d03, resolution 1.97&Aring;" />
-'''Crystal structure of the G91S mutant of the NNA7 Fab'''<br />
-==Overview==
+==Crystal structure of the G91S mutant of the NNA7 Fab==
-The NNA7 Fab antibody fragment recognizes the human N-type blood-group, antigen comprised of the N-terminal glycopeptide of glycophorin A (GPA). A, mutant form of this Fab fragment, NNA7-G91S, exhibits markedly reduced, antigen binding. To provide insight into how these Fab fragments recognize, this glycopeptide antigen, the crystal structures of NNA7 and NNA7-G91S, were solved and refined to 1.83 and 1.97 A resolution, respectively. Both, molecules are composed of the same heavy (H) chain Fd fragment, but each, contains a slightly different light (L) chain owing to the G91S, substitution. Specifically, the G91S mutation pushes the backbone of the, neighboring H chain away from complementarity-determining region 3 (CDR3), of the L-chain variable region, allowing an additional glycerol, cryoprotectant molecule to enter the antigen-combining site near the, putative location of O-linked glycosylation. Each Fab fragment also, possesses a well defined 2-(N-morpholino)ethanesulfonic acid (MES), molecule trapped in its antigen-combining site, as well as a, crystallographic symmetry-related molecule comprising an amino-acid, sequence that is virtually identical to the N-terminus of GPA. The MES, molecule interacts with the H-chain CDR in a manner reminiscent of, antibody-carbohydrate complexes. These results suggest a model for, recognition of the glycopeptide antigen that accounts for the deleterious, effect of the G91S substitution.
+<StructureSection load='2d03' size='340' side='right'caption='[[2d03]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2d03]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D03 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]] 1.97&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=2d03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d03 OCA], [https://pdbe.org/2d03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d03 RCSB], [https://www.ebi.ac.uk/pdbsum/2d03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d03 ProSAT]</span></td></tr>
+</table>
+== 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/d0/2d03_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=2d03 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The NNA7 Fab antibody fragment recognizes the human N-type blood-group antigen comprised of the N-terminal glycopeptide of glycophorin A (GPA). A mutant form of this Fab fragment, NNA7-G91S, exhibits markedly reduced antigen binding. To provide insight into how these Fab fragments recognize this glycopeptide antigen, the crystal structures of NNA7 and NNA7-G91S were solved and refined to 1.83 and 1.97 A resolution, respectively. Both molecules are composed of the same heavy (H) chain Fd fragment, but each contains a slightly different light (L) chain owing to the G91S substitution. Specifically, the G91S mutation pushes the backbone of the neighboring H chain away from complementarity-determining region 3 (CDR3) of the L-chain variable region, allowing an additional glycerol cryoprotectant molecule to enter the antigen-combining site near the putative location of O-linked glycosylation. Each Fab fragment also possesses a well defined 2-(N-morpholino)ethanesulfonic acid (MES) molecule trapped in its antigen-combining site, as well as a crystallographic symmetry-related molecule comprising an amino-acid sequence that is virtually identical to the N-terminus of GPA. The MES molecule interacts with the H-chain CDR in a manner reminiscent of antibody-carbohydrate complexes. These results suggest a model for recognition of the glycopeptide antigen that accounts for the deleterious effect of the G91S substitution.
-==About this Structure==
+Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.,Xie K, Song SC, Spitalnik SL, Wedekind JE Acta Crystallogr D Biol Crystallogr. 2005 Oct;61(Pt 10):1386-94. Epub 2005, Sep 28. PMID:16204891<ref>PMID:16204891</ref>
-D03 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with MES, GOL and PEG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D03 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition., Xie K, Song SC, Spitalnik SL, Wedekind JE, Acta Crystallogr D Biol Crystallogr. 2005 Oct;61(Pt 10):1386-94. Epub 2005, Sep 28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16204891 16204891]
+</div>
+<div class="pdbe-citations 2d03" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Sandbox 20009|Sandbox 20009]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Song SC]]
-[[Category: Song, S.C.]]
+[[Category: Spitalnik SL]]
-[[Category: Spitalnik, S.L.]]
+[[Category: Wedekind JE]]
-[[Category: Wedekind, J.E.]]
+[[Category: Xie K]]
-[[Category: Xie, K.]]
-[[Category: GOL]]
-[[Category: MES]]
-[[Category: PEG]]
-[[Category: antibody]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:48:23 2007''