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1qnz

From Proteopedia

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[[Image:1qnz.gif|left|200px]]<br /><applet load="1qnz" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qnz" />
 
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'''NMR STRUCTURE OF THE 0.5B ANTI-HIV ANTIBODY COMPLEX WITH THE GP120 V3 PEPTIDE'''<br />
 
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==Overview==
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==NMR structure of the 0.5b anti-HIV antibody complex with the gp120 V3 peptide==
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BACKGROUND: The protein 0.5beta is a potent strain-specific human immunodeficiency virus type 1 (HIV-1) neutralizing antibody raised against the entire envelope glycoprotein (gp120) of the HIV-1(IIIB) strain. The epitope recognized by 0.5beta is located within the third hypervariable region (V3) of gp120. Recently, several HIV-1 V3 residues involved in co-receptor utilization and selection were identified. RESULTS: Virtually complete sidechain assignment of the variable fragment (Fv) of 0.5beta in complex with the V3(IIIB) peptide P1053 (RKSIRIQRGPGRAFVTIG, in single-letter amino acid code) was accomplished and the combining site structure of 0.5beta Fv complexed with P1053 was solved using multidimensional nuclear magnetic resonance (NMR). Five of the six complementarity determining regions (CDRs) of the antibody adopt standard canonical conformations, whereas CDR3 of the heavy chain assumes an unexpected fold. The epitope recognized by 0.5beta encompasses 14 of the 18 P1053 residues. The bound peptide assumes a beta-hairpin conformation with a QRGPGR loop located at the very center of the binding pocket. The Fv and peptide surface areas buried upon binding are 601 A and 743 A(2), respectively, in the 0.5beta Fv-P1053 mean structure. The surface of P1053 interacting with the antibody is more extensive and the V3 peptide orientation in the binding site is significantly different compared with those derived from the crystal structures of a V3 peptide of the HIV-1 MN strain (V3(MN)) complexed to three different anti-peptide antibodies. CONCLUSIONS: The surface of P1053 that is in contact with the anti-protein antibody 0.5beta is likely to correspond to a solvent-exposed region in the native gp120 molecule. Some residues of this region of gp120 are involved in co-receptor binding, and in discrimination between different chemokine receptors utilized by the protein. Several highly variable residues in the V3 loop limit the specificity of the 0.5beta antibody, helping the virus to escape from the immune system. The highly conserved GPG sequence might have a role in maintaining the beta-hairpin conformation of the V3 loop despite insertions, deletions and mutations in the flanking regions.
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<StructureSection load='1qnz' size='340' side='right'caption='[[1qnz]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qnz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QNZ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1qnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnz OCA], [https://pdbe.org/1qnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qnz RCSB], [https://www.ebi.ac.uk/pdbsum/1qnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/HVM06_MOUSE HVM06_MOUSE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qn/1qnz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1qnz ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1QNZ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNZ OCA].
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[Gp120 3D structures|Gp120 3D structures]]
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==Reference==
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface important for co-receptor binding., Tugarinov V, Zvi A, Levy R, Hayek Y, Matsushita S, Anglister J, Structure. 2000 Apr 15;8(4):385-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10801487 10801487]
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__TOC__
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</StructureSection>
[[Category: Human immunodeficiency virus 1]]
[[Category: Human immunodeficiency virus 1]]
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Protein complex]]
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[[Category: Anglister J]]
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[[Category: Anglister, J.]]
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[[Category: Hayek Y]]
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[[Category: Hayek, Y.]]
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[[Category: Levy R]]
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[[Category: Levy, R.]]
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[[Category: Matsushita S]]
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[[Category: Matsushita, S.]]
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[[Category: Tugarinov V]]
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[[Category: Tugarinov, V.]]
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[[Category: Zvi A]]
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[[Category: Zvi, A.]]
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[[Category: antibody]]
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[[Category: binding site]]
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[[Category: v3 peptide]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:41:49 2008''
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Current revision

NMR structure of the 0.5b anti-HIV antibody complex with the gp120 V3 peptide

PDB ID 1qnz

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