6X9U image
Entry Detail
PDB ID:
6X9U
EMDB ID:
Title:
HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and partially deglycosylated by endoglycosidase H, in complex with RM20A3 Fab
Biological Source:
PDB Version:
Deposition Date:
2020-06-03
Release Date:
2020-11-04
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120
Mutations:T332N,A501C
Chain IDs:A
Chain Length:516
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Description:HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
Mutations:I559P,T605C
Chain IDs:B
Chain Length:153
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Description:RM20A3 Fab Heavy Chain
Chain IDs:C (auth: H)
Chain Length:125
Number of Molecules:1
Biological Source:Macaca mulatta
Polymer Type:polypeptide(L)
Description:RM20A3 Fab Light Chain
Chain IDs:D (auth: L)
Chain Length:128
Number of Molecules:1
Biological Source:Macaca mulatta
Ligand Molecules
Primary Citation
Visualization of the HIV-1 Env glycan shield across scales.
Proc.Natl.Acad.Sci.USA 117 28014 28025 (2020)
PMID: 33093196 DOI: 10.1073/pnas.2000260117

Abstact

The dense array of N-linked glycans on the HIV-1 envelope glycoprotein (Env), known as the "glycan shield," is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure-function analysis. Here, we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of interglycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same cell line used for vaccine production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner, we found that highly connected glycan clusters are resistant to digestion and help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.

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Primary Citation of related structures