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- EMDB-27611: BG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb -

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Basic information

Entry
Database: EMDB / ID: EMD-27611
TitleBG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb
Map dataRh.NJ95 wk13 base pAb (main map)
Sample
  • Complex: BG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb
Keywordspolyclonal antibodies / HIV-1 / Env / non-human primate / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTorres JL / Lee WH / Ozorowski G / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144462 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nature / Year: 2022
Title: Long-primed germinal centres with enduring affinity maturation and clonal migration.
Authors: Jeong Hyun Lee / Henry J Sutton / Christopher A Cottrell / Ivy Phung / Gabriel Ozorowski / Leigh M Sewall / Rebecca Nedellec / Catherine Nakao / Murillo Silva / Sara T Richey / Jonathan L ...Authors: Jeong Hyun Lee / Henry J Sutton / Christopher A Cottrell / Ivy Phung / Gabriel Ozorowski / Leigh M Sewall / Rebecca Nedellec / Catherine Nakao / Murillo Silva / Sara T Richey / Jonathan L Torres / Wen-Hsin Lee / Erik Georgeson / Michael Kubitz / Sam Hodges / Tina-Marie Mullen / Yumiko Adachi / Kimberly M Cirelli / Amitinder Kaur / Carolina Allers / Marissa Fahlberg / Brooke F Grasperge / Jason P Dufour / Faith Schiro / Pyone P Aye / Oleksandr Kalyuzhniy / Alessia Liguori / Diane G Carnathan / Guido Silvestri / Xiaoying Shen / David C Montefiori / Ronald S Veazey / Andrew B Ward / Lars Hangartner / Dennis R Burton / Darrell J Irvine / William R Schief / Shane Crotty /
Abstract: Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further ...Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (B) cells that last for at least 6 months. A 186-fold increase in B cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of B cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding B cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells. Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous B cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses.
History
DepositionJul 13, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27611.png

Downloads & links

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Map

FileDownload / File: emd_27611.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRh.NJ95 wk13 base pAb (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: 0.015
Minimum - Maximum-0.020962514 - 0.1015042
Average (Standard dev.)0.00015201142 (±0.0035361035)
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: Rh.NJ95 wk13 base pAb (half map 1)

Fileemd_27611_half_map_1.map
AnnotationRh.NJ95 wk13 base pAb (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rh.NJ95 wk13 base pAb (half map 1)

Fileemd_27611_half_map_2.map
AnnotationRh.NJ95 wk13 base pAb (half map 1)
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.NJ95 wk13 base epitope pAb

EntireName: BG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb
Components
  • Complex: BG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb

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Supramolecule #1: BG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb

SupramoleculeName: BG505 MD39 SOSIP in complex with Rh.NJ95 wk13 base epitope pAb
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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

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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: 200 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
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2200
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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