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- EMDB-24853: Modified BG505 SOSIP-based immunogen RC1 in complex with elicited... -

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Basic information

Entry
Database: EMDB / ID: EMD-24853
TitleModified BG505 SOSIP-based immunogen RC1 in complex with elicited mAb Ab283MUR Fab and 8ANC195 Fab
Map data
Sample
  • Complex: Elicited Ab283MUR Fab in complex with RC1 SOSIP and bNAb 8ANC195 Fab
    • Complex: Ab283MUR Fab
    • Complex: RC1 SOSIP
    • Complex: 8ANC195 Fab
Biological speciesMus musculus (house mouse) / Human immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsAbernathy ME / Bjorkman PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI100148 United States
CitationJournal: Sci Transl Med / Year: 2021
Title: Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env.
Authors: Amelia Escolano / Harry B Gristick / Rajeev Gautam / Andrew T DeLaitsch / Morgan E Abernathy / Zhi Yang / Haoqing Wang / Magnus A G Hoffmann / Yoshiaki Nishimura / Zijun Wang / Nicholas ...Authors: Amelia Escolano / Harry B Gristick / Rajeev Gautam / Andrew T DeLaitsch / Morgan E Abernathy / Zhi Yang / Haoqing Wang / Magnus A G Hoffmann / Yoshiaki Nishimura / Zijun Wang / Nicholas Koranda / Leesa M Kakutani / Han Gao / Priyanthi N P Gnanapragasam / Henna Raina / Ana Gazumyan / Melissa Cipolla / Thiago Y Oliveira / Victor Ramos / Darrell J Irvine / Murillo Silva / Anthony P West / Jennifer R Keeffe / Christopher O Barnes / Michael S Seaman / Michel C Nussenzweig / Malcolm A Martin / Pamela J Bjorkman /
Abstract: Broadly neutralizing antibodies (bNAbs) against HIV-1 develop after prolonged virus and antibody coevolution. Previous studies showed that sequential immunization with a V3-glycan patch germline- ...Broadly neutralizing antibodies (bNAbs) against HIV-1 develop after prolonged virus and antibody coevolution. Previous studies showed that sequential immunization with a V3-glycan patch germline-targeting HIV-1 envelope trimer (Env) followed by variant Envs can reproduce this process in mice carrying V3-glycan bNAb precursor B cells. However, eliciting bNAbs in animals with polyclonal antibody repertoires is more difficult. We used a V3-glycan immunogen multimerized on virus-like particles (VLPs), followed by boosting with increasingly native-like Env-VLPs, to elicit heterologous neutralizing antibodies in nonhuman primates (NHPs). Structures of antibody/Env complexes after prime and boost vaccinations demonstrated target epitope recognition with apparent maturation to accommodate glycans. However, we also observed increasing off-target antibodies with boosting. Eight vaccinated NHPs were subsequently challenged with simian-human immunodeficiency virus (SHIV), and seven of eight animals became infected. The single NHP that remained uninfected after viral challenge exhibited one of the lowest neutralization titers against the challenge virus. These results demonstrate that more potent heterologous neutralization resulting from sequential immunization is necessary for protection in this animal model. Thus, improved prime-boost regimens to increase bNAb potency and stimulate other immune protection mechanisms are essential for developing anti–HIV-1 vaccines.
History
DepositionSep 13, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateApr 6, 2022-
Current statusApr 6, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24853.png

Downloads & links

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Map

FileDownload / File: emd_24853.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.145 Å
Density
Contour LevelBy AUTHOR: 0.0266
Minimum - Maximum-0.0661763 - 0.11152046
Average (Standard dev.)1.7790024e-05 (±0.006012333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 329.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24853_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24853_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24853_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Elicited Ab283MUR Fab in complex with RC1 SOSIP and bNAb 8ANC195 Fab

EntireName: Elicited Ab283MUR Fab in complex with RC1 SOSIP and bNAb 8ANC195 Fab
Components
  • Complex: Elicited Ab283MUR Fab in complex with RC1 SOSIP and bNAb 8ANC195 Fab
    • Complex: Ab283MUR Fab
    • Complex: RC1 SOSIP
    • Complex: 8ANC195 Fab

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Supramolecule #1: Elicited Ab283MUR Fab in complex with RC1 SOSIP and bNAb 8ANC195 Fab

SupramoleculeName: Elicited Ab283MUR Fab in complex with RC1 SOSIP and bNAb 8ANC195 Fab
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 600 KDa

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Supramolecule #2: Ab283MUR Fab

SupramoleculeName: Ab283MUR Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: RC1 SOSIP

SupramoleculeName: RC1 SOSIP / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: 8ANC195 Fab

SupramoleculeName: 8ANC195 Fab / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

Concentration1.35 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.2 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 92225
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5cjx


Details: 60 A low-pass filtered map created using molmap in UCSF Chimera
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8469
FSC plot (resolution estimation)

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