1e6j: Difference between revisions

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-[[Image:1e6j.png|left|200px]]
-<!--
+==Crystal structure of HIV-1 capsid protein (p24) in complex with Fab13B5==
-The line below this paragraph, containing "STRUCTURE_1e6j", creates the "Structure Box" on the page.
+<StructureSection load='1e6j' size='340' side='right'caption='[[1e6j]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1e6j]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/HIV-1_M:B_HXB2R HIV-1 M:B_HXB2R] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. The July 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''HIV Capsid''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_7 10.2210/rcsb_pdb/mom_2013_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6J FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</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=1e6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6j OCA], [https://pdbe.org/1e6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6j RCSB], [https://www.ebi.ac.uk/pdbsum/1e6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6j ProSAT]</span></td></tr>
-{{STRUCTURE_1e6j|  PDB=1e6j  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q99LC4_MOUSE Q99LC4_MOUSE]
+== 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/e6/1e6j_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=1e6j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Elucidating the structural basis of antigen-antibody recognition ideally requires a structural comparison of free and complexed components. To this end we have studied a mouse monoclonal antibody, denoted 13B5, raised against p24, the capsid protein of HIV-1. We have previously described the first crystal structure of intact p24 as visualized in the Fab13B5-p24 complex. Here we report the structure of the uncomplexed Fab13B5 at 1.8 A resolution and analyze the Fab-p24 interface and the conformational changes occurring upon complex formation. RESULTS: Fab13B5 recognizes a nearly continuous epitope comprising a helix-turn-helix motif in the C-terminal domain of p24. Only 4 complementarity-determining regions (CDRs) are in contact with p24 with most interactions being by the heavy chain. Comparison of the free and complexed Fab reveals that structural changes upon binding are localized to a few side chains of CDR-H1 and -H2 but involve a larger, concerted displacement of CDR-H3. Antigen binding is also associated with an 8 degrees relative rotation of the heavy and light chain variable regions. In p24, small conformational changes localized to the turn between the two helices comprising the epitope result from Fab binding. CONCLUSIONS: The relatively small area of contact between Fab13B5 and p24 may be related to the fact that the epitope is a continuous peptide rather than a more complex protein surface and correlates with a relatively low affinity of antigen and antibody. Despite this, a significant quaternary structural change occurs in the Fab upon complex formation, with additional smaller adaptations of both antigen and antibody.
-===CRYSTAL STRUCTURE OF HIV-1 CAPSID PROTEIN (P24) IN COMPLEX WITH FAB13B5===
+Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24.,Monaco-Malbet S, Berthet-Colominas C, Novelli A, Battai N, Piga N, Cheynet V, Mallet F, Cusack S Structure. 2000 Oct 15;8(10):1069-77. PMID:11080628<ref>PMID:11080628</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e6j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11080628}}, adds the Publication Abstract to the page
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11080628 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11080628}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: HIV Capsid]]
-[[1e6j]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6J OCA].
+[[Category: HIV-1 M:B_HXB2R]]
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:11080628</ref><ref group="xtra">PMID:10064580</ref><ref group="xtra">PMID:8251747</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Viruses]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Berthet-Colominas, C.]]
+[[Category: Berthet-Colominas C]]
-[[Category: Cusack, S.]]
+[[Category: Cusack S]]
-[[Category: Mallet, F.]]
+[[Category: Mallet F]]
-[[Category: Monaco, S.]]
+[[Category: Monaco S]]
-[[Category: Novelli, A.]]
+[[Category: Novelli A]]
-[[Category: Sibai, G.]]
+[[Category: Sibai G]]
-[[Category: Antibody]]
-[[Category: Antigen]]
-[[Category: Ca]]
-[[Category: Capsid]]
-[[Category: Fab]]
-[[Category: Hiv-1]]
-[[Category: P24]]
-[[Category: Protein-protein interaction]]
-[[Category: Virus assembly]]