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- EMDB-45102: nsEM map of macaque 32653 week 42 polyclonal Fab in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45102
TitlensEM map of macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 Boost #2 immunogen
Map data3Drefine_1
Sample
  • Complex: macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 Boost #2 immunogen
    • Complex: Polyclonal Fabs
    • Complex: BG505 SOSIP v5.2 Boost #2
KeywordsHIV-1 / Env / NHP / Antibody / Fusion Peptide / Polyclonal / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsPratap PP / Cottrell CA / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI10066 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: bioRxiv / Year: 2023
Title: Focusing antibody responses to the fusion peptide in rhesus macaques.
Authors: Christopher A Cottrell / Payal P Pratap / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Aleksandar Antanasijevic / Gabriel Ozorowski / Leigh M Sewall / Hongmei Gao / Kelli M ...Authors: Christopher A Cottrell / Payal P Pratap / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Aleksandar Antanasijevic / Gabriel Ozorowski / Leigh M Sewall / Hongmei Gao / Kelli M Greene / Joel D Allen / Julia T Ngo / Yury Choe / Bartek Nogal / Murillo Silva / Jinal Bhiman / Matthias Pauthner / Darrell J Irvine / David Montefiori / Max Crispin / Dennis R Burton / Guido Silvestri / Shane Crotty / Andrew B Ward /
Abstract: Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies ...Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to elicit immune responses against the conserved fusion peptide. Antibody specificities and GC responses were tracked longitudinally using electron microscopy polyclonal epitope mapping (EMPEM) and lymph node fine-needle aspirates, respectively. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.
History
DepositionMay 28, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45102.png

Downloads & links

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Map

FileDownload / File: emd_45102.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3Drefine_1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00773
Minimum - Maximum-0.041946713 - 0.0883246
Average (Standard dev.)-0.000060255166 (±0.0057162577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_45102_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_45102_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 B...

EntireName: macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 Boost #2 immunogen
Components
  • Complex: macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 Boost #2 immunogen
    • Complex: Polyclonal Fabs
    • Complex: BG505 SOSIP v5.2 Boost #2

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Supramolecule #1: macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 B...

SupramoleculeName: macaque 32653 week 42 polyclonal Fab in complex with BG505 v5.2 Boost #2 immunogen
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Polyclonal Fabs

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

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Supramolecule #3: BG505 SOSIP v5.2 Boost #2

SupramoleculeName: BG505 SOSIP v5.2 Boost #2 / 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
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMC4H11NO3Tris hydrochloride
StainingType: NEGATIVE / Material: Uranyl Formate
GridModel: EMS Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm

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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: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 5497
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)

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