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4npy

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Revision as of 02:22, 5 August 2016

Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody

Structural highlights

4npy is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	4jy4, 4jy5, 4jy6, 4fqc, 4fqq, 4nco, 4fq1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Broadly neutralizing HIV antibodies (bnAbs) are typically highly somatically mutated, raising doubts as to whether they can be elicited by vaccination. We used 454 sequencing and designed a novel phylogenetic method to model lineage evolution of the bnAbs PGT121-134 and found a positive correlation between the level of somatic hypermutation (SHM) and the development of neutralization breadth and potency. Strikingly, putative intermediates were characterized that show approximately half the mutation level of PGT121-134 but were still capable of neutralizing roughly 40-80% of PGT121-134 sensitive viruses in a 74-virus panel at median titers between 15- and 3-fold higher than PGT121-134. Such antibodies with lower levels of SHM may be more amenable to elicitation through vaccination while still providing noteworthy coverage. Binding characterization indicated a preference of inferred intermediates for native Env binding over monomeric gp120, suggesting that the PGT121-134 lineage may have been selected for binding to native Env at some point during maturation. Analysis of glycan-dependent neutralization for inferred intermediates identified additional adjacent glycans that comprise the epitope and suggests changes in glycan dependency or recognition over the course of affinity maturation for this lineage. Finally, patterns of neutralization of inferred bnAb intermediates suggest hypotheses as to how SHM may lead to potent and broad HIV neutralization and provide important clues for immunogen design.

The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies.,Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P PLoS Pathog. 2013 Nov;9(11):e1003754. doi: 10.1371/journal.ppat.1003754. Epub, 2013 Nov 21. PMID:24278016^[1]

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

References

↑ Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P. The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies. PLoS Pathog. 2013 Nov;9(11):e1003754. doi: 10.1371/journal.ppat.1003754. Epub, 2013 Nov 21. PMID:24278016 doi:http://dx.doi.org/10.1371/journal.ppat.1003754

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4npy"

@@ Line 1: / Line 1: @@
 ==Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody==
 <StructureSection load='4npy' size='340' side='right' caption='[[4npy]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jy4|4jy4]], [[4jy5|4jy5]], [[4jy6|4jy6]], [[4fqc|4fqc]], [[4fqq|4fqq]], [[4nco|4nco]], [[4fq1|4fq1]]</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=4npy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4npy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4npy RCSB], [http://www.ebi.ac.uk/pdbsum/4npy 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=4npy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4npy OCA], [http://pdbe.org/4npy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4npy RCSB], [http://www.ebi.ac.uk/pdbsum/4npy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4npy ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 16: / Line 17: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4npy" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4npy

From Proteopedia

Revision as of 02:22, 5 August 2016

Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody

Structural highlights

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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