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- EMDB-29334: N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at d... -

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Basic information

Entry
Database: EMDB / ID: EMD-29334
TitleN332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at day 16 from mRNA immunized wild type mice
Map dataday 16 V1V3 response main map
Sample
  • Complex: N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at day 16 from mRNA immunized wild type mice
    • Complex: V1V3 polyclonal Fabs
    • Complex: N332-GT5 SOSIP
Keywordspolyclonal antibodies / mouse antibody / germline targeting / HIV-1 / vaccine design / VIRAL PROTEIN
Biological speciesMus musculus (house mouse) / Human immunodeficiency virus
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTorres JL / Jackson AM / Ozorowski G / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1115782/INV-002916 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144462 United States
CitationJournal: Science / Year: 2024
Title: mRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies.
Authors: Zhenfei Xie / Ying-Cing Lin / Jon M Steichen / Gabriel Ozorowski / Sven Kratochvil / Rashmi Ray / Jonathan L Torres / Alessia Liguori / Oleksandr Kalyuzhniy / Xuesong Wang / John E Warner / ...Authors: Zhenfei Xie / Ying-Cing Lin / Jon M Steichen / Gabriel Ozorowski / Sven Kratochvil / Rashmi Ray / Jonathan L Torres / Alessia Liguori / Oleksandr Kalyuzhniy / Xuesong Wang / John E Warner / Stephanie R Weldon / Gordon A Dale / Kathrin H Kirsch / Usha Nair / Sabyasachi Baboo / Erik Georgeson / Yumiko Adachi / Michael Kubitz / Abigail M Jackson / Sara T Richey / Reid M Volk / Jeong Hyun Lee / Jolene K Diedrich / Thavaleak Prum / Samantha Falcone / Sunny Himansu / Andrea Carfi / John R Yates / James C Paulson / Devin Sok / Andrew B Ward / William R Schief / Facundo D Batista /
Abstract: Germline-targeting (GT) HIV vaccine strategies are predicated on deriving broadly neutralizing antibodies (bnAbs) through multiple boost immunogens. However, as the recruitment of memory B cells ...Germline-targeting (GT) HIV vaccine strategies are predicated on deriving broadly neutralizing antibodies (bnAbs) through multiple boost immunogens. However, as the recruitment of memory B cells (MBCs) to germinal centers (GCs) is inefficient and may be derailed by serum antibody-induced epitope masking, driving further B cell receptor (BCR) modification in GC-experienced B cells after boosting poses a challenge. Using humanized immunoglobulin knockin mice, we found that GT protein trimer immunogen N332-GT5 could prime inferred-germline precursors to the V3-glycan-targeted bnAb BG18 and that B cells primed by N332-GT5 were effectively boosted by either of two novel protein immunogens designed to have minimum cross-reactivity with the off-target V1-binding responses. The delivery of the prime and boost immunogens as messenger RNA lipid nanoparticles (mRNA-LNPs) generated long-lasting GCs, somatic hypermutation, and affinity maturation and may be an effective tool in HIV vaccine development.
History
DepositionDec 28, 2022-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29334.png

Downloads & links

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Map

FileDownload / File: emd_29334.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationday 16 V1V3 response main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 192 pix.
= 395.52 Å		2.06 Å/pix.
x 192 pix.
= 395.52 Å		2.06 Å/pix.
x 192 pix.
= 395.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.040949624 - 0.09003015
Average (Standard dev.)0.000107767235 (±0.0046797376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: day 16 V1V3 response half map A

Fileemd_29334_half_map_1.map
Annotationday 16 V1V3 response half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: day 16 V1V3 response half map B

Fileemd_29334_half_map_2.map
Annotationday 16 V1V3 response half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at d...

EntireName: N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at day 16 from mRNA immunized wild type mice
Components
  • Complex: N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at day 16 from mRNA immunized wild type mice
    • Complex: V1V3 polyclonal Fabs
    • Complex: N332-GT5 SOSIP

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Supramolecule #1: N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at d...

SupramoleculeName: N332-GT5 SOSIP in complex with V1V3 polyclonal Fabs isolated at day 16 from mRNA immunized wild type mice
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: V1V3 polyclonal Fabs

SupramoleculeName: V1V3 polyclonal Fabs / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: N332-GT5 SOSIP

SupramoleculeName: N332-GT5 SOSIP / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus

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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

Concentration0.03 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: PDB coordinates converted to map using UCSF Chimera molmap and low pass filtered to 40 Angstrom
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 5410
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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