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3egs

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Revision as of 21:33, 2 December 2018

Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671 soaked in ammonium sulfate

Structural highlights

3egs is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	3d0l, 3drq, 3drt
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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.

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^[1]

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

References

↑ de la Arada I, Julien JP, de la Torre BG, Huarte N, Andreu D, Pai EF, Arrondo JL, Nieva JL. Structural constraints imposed by the conserved fusion peptide on the HIV-1 gp41 epitope recognized by the broadly neutralizing antibody 2F5. J Phys Chem B. 2009 Oct 15;113(41):13626-37. PMID:19754136 doi:10.1021/jp905965h

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671 soaked in ammonium sulfate==
 <StructureSection load='3egs' size='340' side='right' caption='[[3egs]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3d0l|3d0l]], [[3drq|3drq]], [[3drt|3drt]]</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=3egs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3egs OCA], [http://pdbe.org/3egs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3egs RCSB], [http://www.ebi.ac.uk/pdbsum/3egs PDBsum]</span></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=3egs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3egs OCA], [http://pdbe.org/3egs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3egs RCSB], [http://www.ebi.ac.uk/pdbsum/3egs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3egs ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eg/3egs_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eg/3egs_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 ==See Also==
-*[[Antibody|Antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
 == References ==
 <references/>

3egs

From Proteopedia

Revision as of 21:33, 2 December 2018

Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671 soaked in ammonium sulfate

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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