3lex

From Proteopedia

(Difference between revisions)

Current revision

2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with HIV-1 GP41

Structural highlights

3lex is a 6 chain structure with sequence from Human immunodeficiency virus 1 and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.97Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9IJQ0_9HIV1

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Elicitation of antibodies against targets that are immunorecessive, cryptic, or transient in their native context has been a challenge for vaccine design. Here we demonstrate the elicitation of structure-specific antibodies against the HIV-1 gp41 epitope of the broadly neutralizing antibody 2F5. This conformationally flexible region of gp41 assumes mostly helical conformations but adopts a kinked, extended structure when bound by antibody 2F5. Computational techniques were employed to transplant the 2F5 epitope into select acceptor scaffolds. The resultant "2F5-epitope scaffolds" possessed nanomolar affinity for antibody 2F5 and a range of epitope flexibilities and antigenic specificities. Crystallographic characterization of the epitope scaffold with highest affinity and antigenic discrimination confirmed good to near perfect attainment of the target conformation for the gp41 molecular graft in free and 2F5-bound states, respectively. Animals immunized with 2F5-epitope scaffolds showed levels of graft-specific immune responses that correlated with graft flexibility (p < 0.04), while antibody responses against the graft-as dissected residue-by-residue with alanine substitutions-resembled more closely those of 2F5 than sera elicited with flexible or cyclized peptides, a resemblance heightened by heterologous prime-boost. Lastly, crystal structures of a gp41 peptide in complex with monoclonal antibodies elicited by the 2F5-epitope scaffolds revealed that the elicited antibodies induce gp41 to assume its 2F5-recognized shape. Epitope scaffolds thus provide a means to elicit antibodies that recognize a predetermined target shape and sequence, even if that shape is transient in nature, and a means by which to dissect factors influencing such elicitation.

Elicitation of structure-specific antibodies by epitope scaffolds.,Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, Wyatt R, Kwong PD Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17880-7. Epub 2010 Sep 27. PMID:20876137^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, Wyatt R, Kwong PD. Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17880-7. Epub 2010 Sep 27. PMID:20876137 doi:10.1073/pnas.1004728107

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lex"

@@ Line 3: / Line 3: @@
 <StructureSection load='3lex' size='340' side='right'caption='[[3lex]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lex]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3LEX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lex]] is a 6 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 crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LEX FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3les|3les]], [[3lev|3lev]], [[3ley|3ley]], [[1tji|1tji]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3lex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lex OCA], [http://pdbe.org/3lex PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lex RCSB], [http://www.ebi.ac.uk/pdbsum/3lex PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lex ProSAT]</span></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=3lex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lex OCA], [https://pdbe.org/3lex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lex RCSB], [https://www.ebi.ac.uk/pdbsum/3lex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lex ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9IJQ0_9HIV1 Q9IJQ0_9HIV1]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3lex_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
+[[Category: Human immunodeficiency virus 1]]
 [[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Baker, D]]
+[[Category: Baker D]]
-[[Category: Guenaga, F J]]
+[[Category: Guenaga FJ]]
-[[Category: Kwong, P D]]
+[[Category: Kwong PD]]
-[[Category: Ofek, G]]
+[[Category: Ofek G]]
-[[Category: Schief, W R]]
+[[Category: Schief WR]]
-[[Category: Skinner, J]]
+[[Category: Skinner J]]
-[[Category: Wyatt, R]]
+[[Category: Wyatt R]]
-[[Category: Envelope protein]]
-[[Category: Epitope]]
-[[Category: Gp-41]]
-[[Category: Graft]]
-[[Category: Hiv-1]]
-[[Category: Immune system]]
-[[Category: Monoclonal antibody]]
-[[Category: Re-elcitation]]
-[[Category: Scaffold]]
-[[Category: Transplant]]
-[[Category: Vaccine design]]

3lex

From Proteopedia

Current revision

2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with HIV-1 GP41

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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