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- EMDB-40252: BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole a... -

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Basic information

Entry
Database: EMDB / ID: EMD-40252
TitleBG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
Map datamain map
Sample
  • Complex: BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
    • Complex: Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
    • Complex: BG505 MD39 SOSIP
Keywordspolyclonal antibodies / EMPEM / HIV-1 / vaccine / non-human primate / Env / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsLee WS / Ozorowski G / Torres JL / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144462 United States
CitationJournal: Nat Commun / Year: 2023
Title: A combined adjuvant approach primes robust germinal center responses and humoral immunity in non-human primates.
Authors: Ivy Phung / Kristen A Rodrigues / Ester Marina-Zárate / Laura Maiorino / Bapi Pahar / Wen-Hsin Lee / Mariane Melo / Amitinder Kaur / Carolina Allers / Marissa Fahlberg / Brooke F Grasperge ...Authors: Ivy Phung / Kristen A Rodrigues / Ester Marina-Zárate / Laura Maiorino / Bapi Pahar / Wen-Hsin Lee / Mariane Melo / Amitinder Kaur / Carolina Allers / Marissa Fahlberg / Brooke F Grasperge / Jason P Dufour / Faith Schiro / Pyone P Aye / Paul G Lopez / Jonathan L Torres / Gabriel Ozorowski / Saman Eskandarzadeh / Michael Kubitz / Erik Georgeson / Bettina Groschel / Rebecca Nedellec / Michael Bick / Katarzyna Kaczmarek Michaels / Hongmei Gao / Xiaoying Shen / Diane G Carnathan / Guido Silvestri / David C Montefiori / Andrew B Ward / Lars Hangartner / Ronald S Veazey / Dennis R Burton / William R Schief / Darrell J Irvine / Shane Crotty /
Abstract: Adjuvants and antigen delivery kinetics can profoundly influence B cell responses and should be critically considered in rational vaccine design, particularly for difficult neutralizing antibody ...Adjuvants and antigen delivery kinetics can profoundly influence B cell responses and should be critically considered in rational vaccine design, particularly for difficult neutralizing antibody targets such as human immunodeficiency virus (HIV). Antigen kinetics can change depending on the delivery method. To promote extended immunogen bioavailability and to present antigen in a multivalent form, native-HIV Env trimers are modified with short phosphoserine peptide linkers that promote tight binding to aluminum hydroxide (pSer:alum). Here we explore the use of a combined adjuvant approach that incorporates pSer:alum-mediated antigen delivery with potent adjuvants (SMNP, 3M-052) in an extensive head-to-head comparison study with conventional alum to assess germinal center (GC) and humoral immune responses. Priming with pSer:alum plus SMNP induces additive effects that enhance the magnitude and persistence of GCs, which correlate with better GC-T cell help. Autologous HIV-neutralizing antibody titers are improved in SMNP-immunized animals after two immunizations. Over 9 months after priming immunization of pSer:alum with either SMNP or 3M-052, robust Env-specific bone marrow plasma cells (BM B) are observed. Furthermore, pSer-modification of Env trimer reduce targeting towards immunodominant non-neutralizing epitopes. The study shows that a combined adjuvant approach can augment humoral immunity by modulating immunodominance and shows promise for clinical translation.
History
DepositionMar 30, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40252.png

Downloads & links

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Map

FileDownload / File: emd_40252.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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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: 0.015
Minimum - Maximum-0.020273294 - 0.08490045
Average (Standard dev.)-0.000018779065 (±0.003498805)
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: half map A

Fileemd_40252_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40252_half_map_2.map
Annotationhalf 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 : BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole a...

EntireName: BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
Components
  • Complex: BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
    • Complex: Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
    • Complex: BG505 MD39 SOSIP

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Supramolecule #1: BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole a...

SupramoleculeName: BG505 MD39 SOSIP in complex with Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
type: complex / ID: 1 / Parent: 0
Details: Polyclonal antibodies isolated from serum of non-human primates, digested to Fab, and complexed with HIV-1 GT1.1 BG505 SOSIP.664 Env

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Supramolecule #2: Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies

SupramoleculeName: Rh.NK04 wk12 gp120 glycan hole and base epitope polyclonal antibodies
type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: BG505 MD39 SOSIP

SupramoleculeName: BG505 MD39 SOSIP / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1

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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

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl formate / Details: 2% w/v uranyl formate
GridModel: Homemade / Support film - Material: PARLODION

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
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: simulated map generated from PDB coordinates and low pass filtered
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 4012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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