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- EMDB-22054: Negative stain EM map of SUDV GPdMuc in complex with EA97 -

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Basic information

Entry
Database: EMDB / ID: EMD-22054
TitleNegative stain EM map of SUDV GPdMuc in complex with EA97
Map dataNegative stain EM map of SUDV GPdMuc in complex with EA97 Fab
SampleSUDV GPdMuc in complex with EA97 != EA97 antibody

SUDV GPdMuc in complex with EA97

  • Complex: SUDV GPdMuc in complex with EA97
    • Complex: EA97 antibody
    • Complex: SUDV GPdMuc trimer
Biological speciesMacaca mulatta (Rhesus monkey) / Sudan ebolavirus
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsTurner HL / Ward AB
CitationJournal: J Virol / Year: 2021
Title: Prominent Neutralizing Antibody Response Targeting the Glycoprotein Subunit Interface Elicited by Immunization.
Authors: Yimeng Wang / Katie A Howell / Jennifer Brannan / Krystle N Agans / Hannah L Turner / Ariel S Wirchnianski / Shweta Kailasan / Marnie Fusco / Andrey Galkin / Chi-I Chiang / Xuelian Zhao / ...Authors: Yimeng Wang / Katie A Howell / Jennifer Brannan / Krystle N Agans / Hannah L Turner / Ariel S Wirchnianski / Shweta Kailasan / Marnie Fusco / Andrey Galkin / Chi-I Chiang / Xuelian Zhao / Erica Ollmann Saphire / Kartik Chandran / Andrew B Ward / John M Dye / M Javad Aman / Thomas W Geisbert / Yuxing Li /
Abstract: The severe death toll caused by the recent outbreak of Ebola virus disease reinforces the importance of developing ebolavirus prevention and treatment strategies. Here, we have explored the ...The severe death toll caused by the recent outbreak of Ebola virus disease reinforces the importance of developing ebolavirus prevention and treatment strategies. Here, we have explored the immunogenicity of a novel immunization regimen priming with vesicular stomatitis virus particles bearing Sudan Ebola virus (SUDV) glycoprotein (GP) that consists of GP1 & GP2 subunits and boosting with soluble SUDV GP in macaques, which developed robust neutralizing antibody (nAb) responses following immunizations. Moreover, EB46, a protective nAb isolated from one of the immune macaques, is found to target the GP1/GP2 interface, with GP-binding mode and neutralization mechanism similar to a number of ebolavirus nAbs from human and mouse, indicating that the ebolavirus GP1/GP2 interface is a common immunological target in different species. Importantly, selected immune macaque polyclonal sera showed nAb specificity similar to EB46 at substantial titers, suggesting that the GP1/GP2 interface region is a viable target for ebolavirus vaccine. The elicitation of sustained neutralizing antibody (nAb) responses against diverse ebolavirus strains remains as a high priority for the vaccine field. The most clinically advanced rVSV-ZEBOV vaccine could elicit moderate nAb responses against only one ebolavirus strain, EBOV, among the five ebolavirus strains, which last less than 6 months. Boost immunization strategies are desirable to effectively recall the rVSV vector-primed nAb responses to prevent infections in prospective epidemics, while an in-depth understanding of the specificity of immunization-elicited nAb responses is essential for improving vaccine performance. Here, using non-human primate animal model, we demonstrated that booster immunization with a stabilized trimeric soluble form of recombinant glycoprotein derived from the ebolavirus Sudan strain following the priming rVSV vector immunization led to robust nAb responses that substantially map to the subunit interface of ebolavirus glycoprotein, a common B cell repertoire target of multiple species including primates and rodents.
History
DepositionMay 26, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22054.png

Downloads & links

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Map

FileDownload / File: emd_22054.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of SUDV GPdMuc in complex with EA97 Fab
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 0.0194 / Movie #1: 0.0194
Minimum - Maximum-0.041787837 - 0.09936544
Average (Standard dev.)0.00055736856 (±0.007011943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0420.0990.001

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Supplemental data

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Sample components

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Entire : SUDV GPdMuc in complex with EA97

EntireName: SUDV GPdMuc in complex with EA97
Components
  • Complex: SUDV GPdMuc in complex with EA97
    • Complex: EA97 antibody
    • Complex: SUDV GPdMuc trimer

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Supramolecule #2: EA97 antibody

SupramoleculeName: EA97 antibody / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: SUDV GPdMuc trimer

SupramoleculeName: SUDV GPdMuc trimer / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Sudan ebolavirus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #1: SUDV GPdMuc in complex with EA97

SupramoleculeName: SUDV GPdMuc in complex with EA97 / type: complex / ID: 1 / Parent: 0

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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: 7.4
StainingType: NEGATIVE / Material: uranyl formate
GridDetails: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: -1.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
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:

3csy

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 35772

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