1yc7: Difference between revisions

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[[Image:1yc7.gif|left|200px]]


{{Structure
==cAbAn33 VHH fragment against VSG==
|PDB= 1yc7 |SIZE=350|CAPTION= <scene name='initialview01'>1yc7</scene>, resolution 1.6&Aring;
<StructureSection load='1yc7' size='340' side='right'caption='[[1yc7]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
<table><tr><td colspan='2'>[[1yc7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YC7 FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
|GENE=  
<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>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yc7 OCA], [https://pdbe.org/1yc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yc7 RCSB], [https://www.ebi.ac.uk/pdbsum/1yc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yc7 ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yc7 OCA], [http://www.ebi.ac.uk/pdbsum/1yc7 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yc7 RCSB]</span>
== 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/yc/1yc7_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=1yc7 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Heavy chain only antibodies of camelids bind their antigens with a single domain, the VHH, which acquired adaptations relative to classical VHs to function in the absence of a VL partner. Additional CDR loop conformations, outside the canonical loop structures of VHs, broaden the repertoire of the antigen-binding site. The combined effects of part of the CDR3 that folds over the "former" VL binding site and framework-2 mutations to more hydrophilic amino acids, enhance the solubility of VHH domains and prevent VL pairing. cAbAn33, a VHH domain specific for the carbohydrate moiety of the variant surface glycoprotein of trypanosomes, has a short CDR3 loop that does not cover the former VL binding site as well as a VH-specific Trp47 instead of the VHH-specific Gly47. Resurfacing its framework-2 region (mutations Tyr37Val, Glu44Gly and Arg45Leu) to mimic that of a human VH restores the VL binding capacity. In solution, the humanised VHH behaves as a soluble, monomeric entity, albeit with reduced thermodynamic stability and affinity for its antigen. Comparison of the crystal structures of cAbAn33 and its humanised derivative reveals steric hindrance exerted by VHH-specific residues Tyr37 and Arg45 that prevent the VL domain pairing, whereas Glu44 and Arg45 are key elements to avoid insolubility of the domain.


'''cAbAn33 VHH fragment against VSG'''
Antigen binding and solubility effects upon the veneering of a camel VHH in framework-2 to mimic a VH.,Conrath K, Vincke C, Stijlemans B, Schymkowitz J, Decanniere K, Wyns L, Muyldermans S, Loris R J Mol Biol. 2005 Jul 1;350(1):112-25. PMID:15913651<ref>PMID:15913651</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1yc7" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Heavy chain only antibodies of camelids bind their antigens with a single domain, the VHH, which acquired adaptations relative to classical VHs to function in the absence of a VL partner. Additional CDR loop conformations, outside the canonical loop structures of VHs, broaden the repertoire of the antigen-binding site. The combined effects of part of the CDR3 that folds over the "former" VL binding site and framework-2 mutations to more hydrophilic amino acids, enhance the solubility of VHH domains and prevent VL pairing. cAbAn33, a VHH domain specific for the carbohydrate moiety of the variant surface glycoprotein of trypanosomes, has a short CDR3 loop that does not cover the former VL binding site as well as a VH-specific Trp47 instead of the VHH-specific Gly47. Resurfacing its framework-2 region (mutations Tyr37Val, Glu44Gly and Arg45Leu) to mimic that of a human VH restores the VL binding capacity. In solution, the humanised VHH behaves as a soluble, monomeric entity, albeit with reduced thermodynamic stability and affinity for its antigen. Comparison of the crystal structures of cAbAn33 and its humanised derivative reveals steric hindrance exerted by VHH-specific residues Tyr37 and Arg45 that prevent the VL domain pairing, whereas Glu44 and Arg45 are key elements to avoid insolubility of the domain.
*[[Antibody 3D structures|Antibody 3D structures]]
 
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
==About this Structure==
== References ==
1YC7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YC7 OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
Antigen binding and solubility effects upon the veneering of a camel VHH in framework-2 to mimic a VH., Conrath K, Vincke C, Stijlemans B, Schymkowitz J, Decanniere K, Wyns L, Muyldermans S, Loris R, J Mol Biol. 2005 Jul 1;350(1):112-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15913651 15913651]
[[Category: Camelus dromedarius]]
[[Category: Camelus dromedarius]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Conrath, K.]]
[[Category: Conrath K]]
[[Category: Loris, R.]]
[[Category: Loris R]]
[[Category: Muyldermans, S.]]
[[Category: Muyldermans S]]
[[Category: Schymkowitz, J.]]
[[Category: Schymkowitz J]]
[[Category: Stijlemans, B.]]
[[Category: Stijlemans B]]
[[Category: Vincke, C.]]
[[Category: Vincke C]]
[[Category: Wyns, L.]]
[[Category: Wyns L]]
[[Category: antibody]]
[[Category: camel antibody]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:02:26 2008''
Retrieved from "https://proteopedia.org/1yc7"