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3dro

From Proteopedia

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Current revision

Crystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN grown in ammonium sulfate

Structural highlights

3dro is a 3 chain structure with sequence from Homo sapiens and Human immunodeficiency virus 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6PYX1_HUMAN

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

2F5 is a monoclonal antibody with potent and broadly neutralizing activity against HIV-1. It targets the membrane-proximal external region (MPER) of the gp41 subunit of the envelope glycoprotein and interferes with the process of fusion between viral and host cell membranes. This study presents eight 2F5 F(ab)' crystal structures in complex with various gp41 peptide epitopes. These structures reveal several key features of this antibody-antigen interaction. (1) Whenever free of contacts caused by crystal artifacts, the extended complementarity-determining region H3 loop is mobile; this is true for ligand-free and epitope-bound forms. (2) The interaction between the antibody and the gp41 ELDKWA epitope core is absolutely critical, and there are also close and specific contacts with residues located N-terminal to the epitope core. (3) Residues located at the C-terminus of the gp41 ELDKWA core do not interact as tightly with the antibody. However, in the presence of a larger peptide containing the gp41 fusion peptide segment, these residues adopt a conformation consistent with the start of an alpha-helix. (4) At high sulfate concentrations, the electron density maps of 2F5 F(ab)'-peptide complexes contain a peak that may mark a binding site for phosphate groups of negatively charged lipid headgroups. The refined atomic-level details of 2F5 paratope-epitope interactions revealed here should contribute to a better understanding of the mechanism of 2F5-based virus neutralization, in general, and prove important for the design of potential vaccine candidates intended to elicit 2F5-like antibody production.

Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.,Julien JP, Bryson S, Nieva JL, Pai EF J Mol Biol. 2008 Dec 12;384(2):377-92. Epub 2008 Sep 18. PMID:18824005^[1]

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

References

↑ Julien JP, Bryson S, Nieva JL, Pai EF. Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site. J Mol Biol. 2008 Dec 12;384(2):377-92. Epub 2008 Sep 18. PMID:18824005 doi:10.1016/j.jmb.2008.09.024

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/3dro"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN grown in ammonium sulfate==
-<StructureSection load='3dro' size='340' side='right' caption='[[3dro]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+<StructureSection load='3dro' size='340' side='right'caption='[[3dro]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dro]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DRO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DRO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dro]] 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=3DRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DRO FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2p8m|2p8m]], [[3drq|3drq]], [[3drt|3drt]], [[3drv|3drv]]</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]] 3.9&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dro OCA], [http://pdbe.org/3dro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dro RCSB], [http://www.ebi.ac.uk/pdbsum/3dro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dro 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=3dro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dro OCA], [https://pdbe.org/3dro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dro RCSB], [https://www.ebi.ac.uk/pdbsum/3dro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dro ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q5S532_9HIV1 Q5S532_9HIV1]] The envelope glyprotein gp160 precursor down-modulates cell surface CD4 antigen by interacting with it in the endoplasmic reticulum and blocking its transport to the cell surface (By similarity).[RuleBase:RU004292][SAAS:SAAS000328_004_020447]  The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells. Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells. This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves (By similarity).
+[https://www.uniprot.org/uniprot/Q6PYX1_HUMAN Q6PYX1_HUMAN]
 == 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/3dro_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dro_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[3D structures of antibody|3D structures of antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of human antibody|3D structures of human antibody]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Bryson, S]]
+[[Category: Human immunodeficiency virus 1]]
-[[Category: Julien, J P]]
+[[Category: Large Structures]]
-[[Category: Pai, E F]]
+[[Category: Bryson S]]
-[[Category: Gp41]]
+[[Category: Julien J-P]]
-[[Category: Hiv-1]]
+[[Category: Pai EF]]
-[[Category: Immune system]]
-[[Category: Nmab]]

3dro

From Proteopedia

Current revision

Crystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN grown in ammonium sulfate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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