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- EMDB-22179: C3 symmetric BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-22179
TitleC3 symmetric BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
Map dataC3 symmetric BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
Sample
  • Complex: BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
    • Complex: BG505 SOSIPv5.2
    • Complex: PGT122
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 speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsCottrell CA / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al131873 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 United States
CitationJournal: Cell Rep / Year: 2021
Title: Enhancing glycan occupancy of soluble HIV-1 envelope trimers to mimic the native viral spike.
Authors: Ronald Derking / Joel D Allen / Christopher A Cottrell / Kwinten Sliepen / Gemma E Seabright / Wen-Hsin Lee / Yoann Aldon / Kimmo Rantalainen / Aleksandar Antanasijevic / Jeffrey Copps / ...Authors: Ronald Derking / Joel D Allen / Christopher A Cottrell / Kwinten Sliepen / Gemma E Seabright / Wen-Hsin Lee / Yoann Aldon / Kimmo Rantalainen / Aleksandar Antanasijevic / Jeffrey Copps / Anila Yasmeen / Albert Cupo / Victor M Cruz Portillo / Meliawati Poniman / Niki Bol / Patricia van der Woude / Steven W de Taeye / Tom L G M van den Kerkhof / P J Klasse / Gabriel Ozorowski / Marit J van Gils / John P Moore / Andrew B Ward / Max Crispin / Rogier W Sanders /
Abstract: Artificial glycan holes on recombinant Env-based vaccines occur when a potential N-linked glycosylation site (PNGS) is under-occupied, but not on their viral counterparts. Native-like SOSIP trimers, ...Artificial glycan holes on recombinant Env-based vaccines occur when a potential N-linked glycosylation site (PNGS) is under-occupied, but not on their viral counterparts. Native-like SOSIP trimers, including clinical candidates, contain such holes in the glycan shield that induce strain-specific neutralizing antibodies (NAbs) or non-NAbs. To eliminate glycan holes and mimic the glycosylation of native BG505 Env, we replace all 12 NxS sequons on BG505 SOSIP with NxT. All PNGS, except N133 and N160, are nearly fully occupied. Occupancy of the N133 site is increased by changing N133 to NxS, whereas occupancy of the N160 site is restored by reverting the nearby N156 sequon to NxS. Hence, PNGS in close proximity, such as in the N133-N137 and N156-N160 pairs, affect each other's occupancy. We further apply this approach to improve the occupancy of several Env strains. Increasing glycan occupancy should reduce off-target immune responses to vaccine antigens.
History
DepositionJun 17, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateApr 21, 2021-
Current statusApr 21, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22179.png

Downloads & links

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Map

FileDownload / File: emd_22179.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3 symmetric BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.31622958 - 1.2424281
Average (Standard dev.)0.007027685 (±0.0738667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3161.2420.007

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Supplemental data

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Sample components

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Entire : BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs

EntireName: BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
Components
  • Complex: BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
    • Complex: BG505 SOSIPv5.2
    • Complex: PGT122

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Supramolecule #1: BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs

SupramoleculeName: BG505 SOSIPv5.2 in complex with PGT122 and no RM20E1 Fabs
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: BG505 SOSIPv5.2

SupramoleculeName: BG505 SOSIPv5.2 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #3: PGT122

SupramoleculeName: PGT122 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Number images used: 2123
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 1)

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