Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Visualization of the HIV-1 Env glycan shield across scales.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 117, Issue 45, Page 28014-28025, Year 2020
Publish date	Nov 10, 2020
Authors	Zachary T Berndsen / Srirupa Chakraborty / Xiaoning Wang / Christopher A Cottrell / Jonathan L Torres / Jolene K Diedrich / Cesar A López / John R Yates / Marit J van Gils / James C Paulson / Sandrasegaram Gnanakaran / Andrew B Ward /
PubMed Abstract	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 ...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.
External links	Proc Natl Acad Sci U S A / PubMed:33093196 / PubMed Central
Methods	EM (single particle)
Resolution	3.1 - 3.5 Å
Structure data	22108 6x9r EMDB-22108, PDB-6x9r: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in complex with RM20A3 Fab Method: EM (single particle) / Resolution: 3.1 Å 22109 6x9s EMDB-22109, PDB-6x9s: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in stable CHO cells in complex with RM20A3 Fab Method: EM (single particle) / Resolution: 3.1 Å 22110 6x9t EMDB-22110, PDB-6x9t: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293S cells in complex with RM20A3 Fab Method: EM (single particle) / Resolution: 3.2 Å 22111 6x9u EMDB-22111, PDB-6x9u: HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and partially deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Method: EM (single particle) / Resolution: 3.2 Å 22112 6x9v EMDB-22112, PDB-6x9v: HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Method: EM (single particle) / Resolution: 3.5 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	human immunodeficiency virus 1 macaca mulatta (Rhesus monkey)
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / Envelope / glycoprotein / spike / VIRAL PROTEIN-IMMUNE SYSTEM complex / vaccine