This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2cmr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:22, 13 December 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2cmr.png|left|200px]]
 
-
<!--
+
==Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix==
-
The line below this paragraph, containing "STRUCTURE_2cmr", creates the "Structure Box" on the page.
+
<StructureSection load='2cmr' size='340' side='right'caption='[[2cmr]], [[Resolution|resolution]] 2.00&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'>[[2cmr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CMR 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]] 2&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-
{{STRUCTURE_2cmr| PDB=2cmr | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmr OCA], [https://pdbe.org/2cmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cmr RCSB], [https://www.ebi.ac.uk/pdbsum/2cmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cmr ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/D0VWW0_9HIV1 D0VWW0_9HIV1]
 +
== 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/cm/2cmr_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2cmr ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Elicitation of potent and broadly neutralizing antibodies is an important goal in designing an effective human immunodeficiency virus-1 (HIV-1) vaccine. The HIV-1 gp41 inner-core trimer represents a functionally and structurally conserved target for therapeutics. Here we report the 2.0-A-resolution crystal structure of the complex between the antigen-binding fragment of D5, an HIV-1 cross-neutralizing antibody, and 5-helix, a gp41 inner-core mimetic. Both binding and neutralization depend on residues in the D5 CDR H2 loop protruding into the conserved gp41 hydrophobic pocket, as well as a large pocket in D5 surrounding core gp41 residues. Kinetic analysis of D5 mutants with perturbed D5-gp41 interactions suggests that D5 persistence at the fusion intermediate is crucial for neutralization. Thus, our data validate the gp41 N-peptide trimer fusion intermediate as a target for neutralizing antibodies and provide a template for identification of more potent and broadly neutralizing molecules.
-
===CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING ANTIBODY D5 FAB BOUND TO THE GP41 INNER-CORE MIMETIC 5-HELIX===
+
Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody.,Luftig MA, Mattu M, Di Giovine P, Geleziunas R, Hrin R, Barbato G, Bianchi E, Miller MD, Pessi A, Carfi A Nat Struct Mol Biol. 2006 Aug;13(8):740-7. Epub 2006 Jul 23. PMID:16862157<ref>PMID:16862157</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2cmr" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_16862157}}, adds the Publication Abstract to the page
+
*[[Antibody 3D structures|Antibody 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 16862157 is the PubMed ID number.
+
*[[3D structures of human antibody|3D structures of human antibody]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_16862157}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
2CMR is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CMR OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:16862157</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Human immunodeficiency virus 1]]
[[Category: Human immunodeficiency virus 1]]
-
[[Category: Barbato, G.]]
+
[[Category: Large Structures]]
-
[[Category: Bianchi, E.]]
+
[[Category: Barbato G]]
-
[[Category: Carfi, A.]]
+
[[Category: Bianchi E]]
-
[[Category: Geleziunas, R.]]
+
[[Category: Carfi A]]
-
[[Category: Giovine, P Di.]]
+
[[Category: Di Giovine P]]
-
[[Category: Hrin, R.]]
+
[[Category: Geleziunas R]]
-
[[Category: Luftig, M A.]]
+
[[Category: Hrin R]]
-
[[Category: Mattu, M.]]
+
[[Category: Luftig MA]]
-
[[Category: Miller, M D.]]
+
[[Category: Mattu M]]
-
[[Category: Pessi, A.]]
+
[[Category: Miller MD]]
-
[[Category: Aid]]
+
[[Category: Pessi A]]
-
[[Category: Envelope protein]]
+
-
[[Category: Gp41]]
+
-
[[Category: Hiv]]
+
-
[[Category: Immunoglobulin]]
+
-
[[Category: Immunoglobulin complex]]
+
-
[[Category: Immunoglobulin domain]]
+
-
[[Category: Membrane]]
+
-
[[Category: Mhc i]]
+
-
[[Category: Neutralization]]
+
-
[[Category: Transmembrane]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:16:23 2009''
+

Current revision

Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix

PDB ID 2cmr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2cmr"
Personal tools