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5t3x

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Revision as of 11:20, 16 September 2020

3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.

Structural highlights

5t3x is a 6 chain structure with sequence from 9hiv1 and Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
NonStd Res:
Related:	5t3z
Gene:	env (9HIV1)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q2N0S6_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).[SAAS:SAAS000328_004_240990]

Publication Abstract from PubMed

HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-A- and 3.9-A-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46-derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs.

Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.,Gristick HB, von Boehmer L, West AP Jr, Schamber M, Gazumyan A, Golijanin J, Seaman MS, Fatkenheuer G, Klein F, Nussenzweig MC, Bjorkman PJ Nat Struct Mol Biol. 2016 Sep 12. doi: 10.1038/nsmb.3291. PMID:27617431^[1]

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

References

↑ Gristick HB, von Boehmer L, West AP Jr, Schamber M, Gazumyan A, Golijanin J, Seaman MS, Fatkenheuer G, Klein F, Nussenzweig MC, Bjorkman PJ. Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nat Struct Mol Biol. 2016 Sep 12. doi: 10.1038/nsmb.3291. PMID:27617431 doi:http://dx.doi.org/10.1038/nsmb.3291

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5t3x"

@@ Line 1: / Line 1: @@
 ==3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.==
-<StructureSection load='5t3x' size='340' side='right' caption='[[5t3x]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+<StructureSection load='5t3x' size='340' side='right'caption='[[5t3x]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5t3x]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T3X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5t3x]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T3X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T3X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t3z|5t3z]]</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=5t3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t3x OCA], [http://pdbe.org/5t3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t3x RCSB], [http://www.ebi.ac.uk/pdbsum/5t3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t3x ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=5t3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t3x OCA], [http://pdbe.org/5t3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t3x RCSB], [http://www.ebi.ac.uk/pdbsum/5t3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t3x ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Bjorkman, P J]]
 [[Category: Gristick, H B]]

5t3x

From Proteopedia

Revision as of 11:20, 16 September 2020

3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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