3ntc

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<StructureSection load='3ntc' size='340' side='right'caption='[[3ntc]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
<StructureSection load='3ntc' size='340' side='right'caption='[[3ntc]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ntc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NTC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3NTC FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ntc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NTC FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3ntc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ntc OCA], [http://pdbe.org/3ntc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ntc RCSB], [http://www.ebi.ac.uk/pdbsum/3ntc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ntc ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ntc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ntc OCA], [https://pdbe.org/3ntc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ntc RCSB], [https://www.ebi.ac.uk/pdbsum/3ntc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ntc ProSAT]</span></td></tr>
</table>
</table>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
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</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=3ntc ConSurf].
</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=3ntc ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Humanized monoclonal antibody KD-247 targets the Gly(312)-Pro(313)-Gly(314)-Arg(315) arch of the third hypervariable (V3) loop of the HIV-1 surface glycoprotein. It potently neutralizes many HIV-1 clade B isolates, but not of other clades. To understand the molecular basis of this specificity, we solved a high-resolution (1.55 A) crystal structure of the KD-247 antigen binding fragment and examined the potential interactions with various V3 loop targets. Unlike most antibodies, KD-247 appears to interact with its target primarily through light chain residues. Several of these interactions involve Arg(315) of the V3 loop. To evaluate the role of light chain residues in the recognition of the V3 loop, we generated 20 variants of KD-247 single-chain variable fragments with mutations in the antigen-binding site. Purified proteins were assessed for V3 loop binding using AlphaScreen technology and for HIV-1 neutralization. Our data revealed that recognition of the clade-specificity defining residue Arg(315) of the V3 loop is based on a network of interactions that involve Tyr(L32), Tyr(L92), and Asn(L27d) that directly interact with Arg(315), thus elucidating the molecular interactions of KD-247 with its V3 loop target.
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Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247.,Kirby KA, Ong YT, Hachiya A, Laughlin TG, Chiang LA, Pan Y, Moran JL, Marchand B, Singh K, Gallazzi F, Quinn TP, Yoshimura K, Murakami T, Matsushita S, Sarafianos SG FASEB J. 2015 Jan;29(1):70-80. doi: 10.1096/fj.14-252262. Epub 2014 Oct 28. PMID:25351987<ref>PMID:25351987</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ntc" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
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*[[Sandbox 20009|Sandbox 20009]]
*[[Sandbox 20009|Sandbox 20009]]
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Revision as of 10:12, 19 May 2021

Crystal structure of KD-247 Fab, an anti-V3 antibody that inhibits HIV-1 Entry

PDB ID 3ntc

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