3drt: Difference between revisions

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-[[Image:3drt.png|left|200px]]
-{{STRUCTURE_3drt|  PDB=3drt  |  SCENE=  }}
+==Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671==
+<StructureSection load='3drt' size='340' side='right'caption='[[3drt]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3drt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DRT 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]] 3.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=3drt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3drt OCA], [https://pdbe.org/3drt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3drt RCSB], [https://www.ebi.ac.uk/pdbsum/3drt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3drt 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/dr/3drt_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=3drt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The HIV-1 gp41 epitope recognized by the broadly neutralizing 2F5 antibody has focused much attention as a suitable target in the design of peptide immunogens. Peptides mimicking the linear 2F5 epitope (2F5ep) are however intrinsically disordered, while the structural constraints existing in the cognate gp41 native structure recognized by the antibody are presently unknown. In recent reports, we have shown that core residues of the amino-terminal fusion peptide (FP) increase MAb2F5 affinity. Here, we have inferred the sequence-specific structural constraints imposed by the FP residues on the 2F5 epitope from the comparison of two hybrid peptides: HybK3, which connects through a flexible tether residues derived from 2F5ep and FP sequences, and scrHybK3, combining 2F5ep and an FP sequence with the conserved core scrambled. Circular dichroism, conventional and two-dimensional correlation infrared spectroscopy, and X-ray diffraction studies revealed specific structural features that were dependent on the exact FP sequence, namely, (i) the production with moderate low polarity of an intermediate folded structure enriched in beta-turns and alpha-helix; (ii) the existence in this intermediate of a thermotropic conformational transition taking place at ca. 18-20 degrees C, consistent with the conversion of 3(10)-helices into beta-turn conformers; and (iii) the presence of a C-terminal alpha-helix in crystals of Fab'-peptide complexes. Those features support the existence of native-like tertiary interactions between FP and 2F5 epitope residues, which might be important to recreate when developing an effective AIDS peptide vaccine.
-===Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671===
+Structural constraints imposed by the conserved fusion peptide on the HIV-1 gp41 epitope recognized by the broadly neutralizing antibody 2F5.,de la Arada I, Julien JP, de la Torre BG, Huarte N, Andreu D, Pai EF, Arrondo JL, Nieva JL J Phys Chem B. 2009 Oct 15;113(41):13626-37. PMID:19754136<ref>PMID:19754136</ref>
-{{ABSTRACT_PUBMED_19754136}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3drt" style="background-color:#fffaf0;"></div>
-[[3drt]] is a 3 chain structure of [[Antibody]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DRT OCA].
 ==See Also==
-*[[Antibody|Antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of human antibody|3D structures of human antibody]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:019754136</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Andreu, D.]]
+[[Category: Large Structures]]
-[[Category: Bryson, S.]]
+[[Category: Andreu D]]
-[[Category: Julien, J P.]]
+[[Category: Bryson S]]
-[[Category: Nieva, J L.]]
+[[Category: Julien J-P]]
-[[Category: Pai, E F.]]
+[[Category: Nieva JL]]
-[[Category: Torre, B G.de la.]]
+[[Category: Pai EF]]
-[[Category: 2f5]]
+[[Category: De la Torre BG]]
-[[Category: Gp41]]
-[[Category: Hiv-1]]
-[[Category: Immune system]]
-[[Category: Nmab]]