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- EMDB-24854: Modified BG505 SOSIP-based immunogen RC1 in complex with elicited... -

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Entry
Database: EMDB / ID: EMD-24854
TitleModified BG505 SOSIP-based immunogen RC1 in complex with elicited mAb Ab1170NHP Fab and 8ANC195 Fab
Map data
Sample
  • Complex: Elicited Ab1170NHP Fab in complex with immunogen RC1 SOSIP and bNAb 8ANC195 Fab
    • Complex: Ab1170NHP Fab
    • Complex: RC1 SOSIP
    • Complex: 8ANC195 Fab
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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_24854.png

Downloads & links

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Map

FileDownload / File: emd_24854.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8972 Å
Density
Contour LevelBy AUTHOR: 0.0146
Minimum - Maximum-0.02473538 - 0.054468945
Average (Standard dev.)0.00017831298 (±0.0031441567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 290.6928 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24854_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: #1

Fileemd_24854_additional_1.map
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Half map: #2

Fileemd_24854_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24854_half_map_2.map
Projections & Slices
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Sample components

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Entire : Elicited Ab1170NHP Fab in complex with immunogen RC1 SOSIP and bN...

EntireName: Elicited Ab1170NHP Fab in complex with immunogen RC1 SOSIP and bNAb 8ANC195 Fab
Components
  • Complex: Elicited Ab1170NHP Fab in complex with immunogen RC1 SOSIP and bNAb 8ANC195 Fab
    • Complex: Ab1170NHP Fab
    • Complex: RC1 SOSIP
    • Complex: 8ANC195 Fab

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Supramolecule #1: Elicited Ab1170NHP Fab in complex with immunogen RC1 SOSIP and bN...

SupramoleculeName: Elicited Ab1170NHP Fab in complex with immunogen RC1 SOSIP and bNAb 8ANC195 Fab
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 600 KDa

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Supramolecule #2: Ab1170NHP Fab

SupramoleculeName: Ab1170NHP Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
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

Concentration0.4 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
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 / Nominal magnification: 45000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 1151 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 170550
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5cjx


Details: 50 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91166
FSC plot (resolution estimation)

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