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- EMDB-24856: Modified BG505 SOSIP-based immunogen RC1 in complex with Rabbit 2... -

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Basic information

Entry
Database: EMDB / ID: EMD-24856
TitleModified BG505 SOSIP-based immunogen RC1 in complex with Rabbit 2249 post-Boost 1 polyclonal Fabs
Map dataSharpened map volume
Sample
  • Complex: Modified BG505 SOSIP-based immunogen RC1 in complex with rabbit 2249 post-Boost 1 polyclonal Fabs
    • Complex: Modified BG505 SOSIP-based immunogen RC1
    • Complex: Rabbit 2249 post-Boost 1 polyclonal Fabs
Biological speciesHuman immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsDeLaitsch AT / Barnes CO / 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_24856.png

Downloads & links

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Map

FileDownload / File: emd_24856.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 256 pix.
= 368.64 Å		1.44 Å/pix.
x 256 pix.
= 368.64 Å		1.44 Å/pix.
x 256 pix.
= 368.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21120042 - 0.6238753
Average (Standard dev.)-0.00466856 (±0.031317797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 368.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Modified BG505 SOSIP-based immunogen RC1 in complex with rabbit 2...

EntireName: Modified BG505 SOSIP-based immunogen RC1 in complex with rabbit 2249 post-Boost 1 polyclonal Fabs
Components
  • Complex: Modified BG505 SOSIP-based immunogen RC1 in complex with rabbit 2249 post-Boost 1 polyclonal Fabs
    • Complex: Modified BG505 SOSIP-based immunogen RC1
    • Complex: Rabbit 2249 post-Boost 1 polyclonal Fabs

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Supramolecule #1: Modified BG505 SOSIP-based immunogen RC1 in complex with rabbit 2...

SupramoleculeName: Modified BG505 SOSIP-based immunogen RC1 in complex with rabbit 2249 post-Boost 1 polyclonal Fabs
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Modified BG505 SOSIP-based immunogen RC1

SupramoleculeName: Modified BG505 SOSIP-based immunogen RC1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Rabbit 2249 post-Boost 1 polyclonal Fabs

SupramoleculeName: Rabbit 2249 post-Boost 1 polyclonal Fabs / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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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: 8
Component:
ConcentrationNameFormula
0.02 MTris
0.15 MSodium ChlorideNaCl
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 1.5% Uranyl Formate
Detailsmonodisperse sample

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 28000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 20549
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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