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- EMDB-22720: nsEM map of the 16055 SOSIP HIV Env trimer in complex with polycl... -

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Basic information

Entry
Database: EMDB / ID: EMD-22720
TitlensEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469
Map datansEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469
Sample
  • Complex: nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469 (Week 22)
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 speciessynthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 12.8 Å
AuthorsWard AB / Antanasijevic A
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: NPJ Vaccines / Year: 2021
Title: Immunofocusing and enhancing autologous Tier-2 HIV-1 neutralization by displaying Env trimers on two-component protein nanoparticles.
Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Marlon de Gast / Joel D Allen / Tom P L Bijl / Anila Yasmeen / Rashmi Ravichandran / Judith A Burger / Gabriel Ozorowski / Jonathan L Torres / ...Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Marlon de Gast / Joel D Allen / Tom P L Bijl / Anila Yasmeen / Rashmi Ravichandran / Judith A Burger / Gabriel Ozorowski / Jonathan L Torres / Celia LaBranche / David C Montefiori / Rajesh P Ringe / Marit J van Gils / John P Moore / Per Johan Klasse / Max Crispin / Neil P King / Andrew B Ward / Rogier W Sanders /
Abstract: The HIV-1 envelope glycoprotein trimer is poorly immunogenic because it is covered by a dense glycan shield. As a result, recombinant Env glycoproteins generally elicit inadequate antibody levels ...The HIV-1 envelope glycoprotein trimer is poorly immunogenic because it is covered by a dense glycan shield. As a result, recombinant Env glycoproteins generally elicit inadequate antibody levels that neutralize clinically relevant, neutralization-resistant (Tier-2) HIV-1 strains. Multivalent antigen presentation on nanoparticles is an established strategy to increase vaccine-driven immune responses. However, due to nanoparticle instability in vivo, the display of non-native Env structures, and the inaccessibility of many neutralizing antibody (NAb) epitopes, the effects of nanoparticle display are generally modest for Env trimers. Here, we generate two-component self-assembling protein nanoparticles presenting twenty SOSIP trimers of the clade C Tier-2 genotype 16055. We show in a rabbit immunization study that these nanoparticles induce 60-fold higher autologous Tier-2 NAb titers than the corresponding SOSIP trimers. Epitope mapping studies reveal that the presentation of 16055 SOSIP trimers on these nanoparticle focuses antibody responses to an immunodominant apical epitope. Thus, these nanoparticles are a promising platform to improve the immunogenicity of Env trimers with apex-proximate NAb epitopes.
History
DepositionSep 26, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 10, 2021-
Current statusMar 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22720.png

Downloads & links

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Map

FileDownload / File: emd_22720.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationnsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 224 pix.
= 396.48 Å		1.77 Å/pix.
x 224 pix.
= 396.48 Å		1.77 Å/pix.
x 224 pix.
= 396.48 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: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0469835 - 0.064235575
Average (Standard dev.)-7.388155e-05 (±0.0031557928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z396.480396.480396.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0470.064-0.000

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Supplemental data

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Sample components

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Entire : nsEM map of the 16055 SOSIP HIV Env trimer in complex with polycl...

EntireName: nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469 (Week 22)
Components
  • Complex: nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469 (Week 22)

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Supramolecule #1: nsEM map of the 16055 SOSIP HIV Env trimer in complex with polycl...

SupramoleculeName: nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2469 (Week 22)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293F / Recombinant plasmid: pPPI4

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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

Concentration0.05 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
25.0 mMTris-HCl
150.0 mMsodium chlorideNaCl

Details: TBS buffer, pH 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
Details: Sample diluted to 0.05 mg/mL. 3 uL was applied onto the grid, blotted off, and then stained with 2% uranyl formate for 60 seconds.
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
Details16055 SOSIP.v8.3 was complexed with the purified polyclonal Fab overnight. The complex was purified using SEC and concentrated. The complex was then diluted in TBS to 0.05mg/ml to be loaded onto an imaging grid.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 62000
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 142785
Startup modelType of model: OTHER / Details: Negative Stain EM map of SOSIP trimer
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 112678
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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Atomic model buiding 1

DetailsNo fitting was performed

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