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- EMDB-23373: Negative stain EM map of RM20C Fab in complex with edc BG505 SOSIP.664 -

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Basic information

Entry
Database: EMDB / ID: EMD-23373
TitleNegative stain EM map of RM20C Fab in complex with edc BG505 SOSIP.664
Map dataNegative stain EM map of RM20C fab in complex with edc BG505 SOSIP.664
Sample
  • Complex: RM20C Fab in complex with edc BG505 SOSIP.664
    • Complex: RM20C Fab
    • Complex: BG505 SOSIP.664
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca sylvanus (Barbary ape) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTurner HL / Ward AB / Cottrell CA
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144462 United States
Bill & Melinda Gates FoundationOPP1115782 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: bioRxiv / Year: 2021
Title: Disassembly of HIV envelope glycoprotein trimer immunogens is driven by antibodies elicited via immunization.
Authors: Hannah L Turner / Raiees Andrabi / Christopher A Cottrell / Sara T Richey / Ge Song / Sean Callaghan / Fabio Anzanello / Tyson J Moyer / Wuhbet Abraham / Mariane Melo / Murillo Silva / ...Authors: Hannah L Turner / Raiees Andrabi / Christopher A Cottrell / Sara T Richey / Ge Song / Sean Callaghan / Fabio Anzanello / Tyson J Moyer / Wuhbet Abraham / Mariane Melo / Murillo Silva / Nicole Scaringi / Eva G Rakasz / Quentin Sattentau / Darrell J Irvine / Dennis R Burton / Andrew B Ward /
Abstract: Rationally designed protein subunit vaccines are being developed for a variety of viruses including influenza, RSV, SARS-CoV-2 and HIV. These vaccines are based on stabilized versions of the primary ...Rationally designed protein subunit vaccines are being developed for a variety of viruses including influenza, RSV, SARS-CoV-2 and HIV. These vaccines are based on stabilized versions of the primary targets of neutralizing antibodies on the viral surface, namely viral fusion glycoproteins. While these immunogens display the epitopes of potent neutralizing antibodies, they also present epitopes recognized by non or weakly neutralizing ("off-target") antibodies. Using our recently developed electron microscopy epitope mapping approach, we have uncovered a phenomenon wherein off-target antibodies elicited by HIV trimer subunit vaccines cause the otherwise highly stabilized trimeric proteins to degrade into cognate protomers. Further, we show that these protomers expose an expanded suite of off-target epitopes, normally occluded inside the prefusion conformation of trimer, that subsequently elicit further off-target antibody responses. Our study provides critical insights for further improvement of HIV subunit trimer vaccines for future rounds of the iterative vaccine design process.
History
DepositionJan 26, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23373.png

Downloads & links

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Map

FileDownload / File: emd_23373.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of RM20C fab in complex with edc BG505 SOSIP.664
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0229 / Movie #1: 0.0229
Minimum - Maximum-0.029512348 - 0.061449762
Average (Standard dev.)0.00050635956 (±0.0053926283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 283.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z283.200283.200283.200
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0300.0610.001

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Supplemental data

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Sample components

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Entire : RM20C Fab in complex with edc BG505 SOSIP.664

EntireName: RM20C Fab in complex with edc BG505 SOSIP.664
Components
  • Complex: RM20C Fab in complex with edc BG505 SOSIP.664
    • Complex: RM20C Fab
    • Complex: BG505 SOSIP.664

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Supramolecule #1: RM20C Fab in complex with edc BG505 SOSIP.664

SupramoleculeName: RM20C Fab in complex with edc BG505 SOSIP.664 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: RM20C Fab

SupramoleculeName: RM20C Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca sylvanus (Barbary ape)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #3: BG505 SOSIP.664

SupramoleculeName: BG505 SOSIP.664 / type: complex / ID: 3 / Parent: 1
Details: Chemically crosslinked using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Number real images: 330 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 132232
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 10484
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)

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