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- EMDB-45834: KZ52 Fab fragment bound to Ebola GP, subtomogram average from a c... -

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Basic information

Entry
Database: EMDB / ID: EMD-45834
TitleKZ52 Fab fragment bound to Ebola GP, subtomogram average from a cylinder mask
Map datalocres map
SampleEbola virus != Ebola virus - Eckron (Zaire, 1976)

Ebola virus

  • Virus: Ebola virus - Eckron (Zaire, 1976)
KeywordsEbola virus-like particles / Human Antibody KZ52 Fab Against Ebola Virus / VIRUS LIKE PARTICLE
Biological speciesEbola virus - Eckron (Zaire, 1976)
Methodsubtomogram averaging / cryo EM / Resolution: 12.7 Å
AuthorsKe Z / Saphire EO / Briggs JAG
Funding support United Kingdom, European Union, Germany, United States, 4 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSIONEuropean Union
Max Planck Society Germany
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
CitationJournal: Nat Commun / Year: 2025
Title: Anti-Ebola virus mAb 3A6 protects highly viremic animals from fatal outcome via binding GP in a position elevated from the virion membrane.
Authors: Kathryn M Hastie / Zhe Li Salie / Zunlong Ke / Peter J Halfmann / Lisa Evans DeWald / Sara McArdle / Ariadna Grinyó / Edgar Davidson / Sharon L Schendel / Chitra Hariharan / Michael J ...Authors: Kathryn M Hastie / Zhe Li Salie / Zunlong Ke / Peter J Halfmann / Lisa Evans DeWald / Sara McArdle / Ariadna Grinyó / Edgar Davidson / Sharon L Schendel / Chitra Hariharan / Michael J Norris / Xiaoying Yu / Chakravarthy Chennareddy / Xiaoli Xiong / Megan Heinrich / Michael R Holbrook / Benjamin Doranz / Ian Crozier / Yoshihiro Kawaoka / Luis M Branco / Jens H Kuhn / John A G Briggs / Gabriella Worwa / Carl W Davis / Rafi Ahmed / Erica Ollmann Saphire /
Abstract: Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP) are the standard of care for Ebola virus disease (EVD). Anti-GP mAbs targeting the stalk and membrane proximal external ...Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP) are the standard of care for Ebola virus disease (EVD). Anti-GP mAbs targeting the stalk and membrane proximal external region (MPER) potently neutralize EBOV in vitro and are protective in a mouse model of EVD. However, their neutralization mechanism is poorly understood because they target a GP epitope that has evaded structural characterization. Using X-ray crystallography and cryo-electron tomography of mAb 3A6 complexed with its stalk-MPER epitope, we reveal a previously undescribed mechanism in which 3A6 binds to a conformation of GP that is lifted from the virion membrane. We further show that in both domestic guinea pig and rhesus monkey EVD models, 3A6 provides therapeutic benefit at high-viremia advanced disease stages and at the lowest dose yet demonstrated for any anti-EBOV mAb-based monotherapy. The findings reported here can guide design of next-generation highly potent anti-EBOV therapeutics and vaccines.
History
DepositionJul 20, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45834.png

Downloads & links

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Map

FileDownload / File: emd_45834.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocres map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.77 Å/pix.
x 128 pix.
= 354.816 Å		2.77 Å/pix.
x 128 pix.
= 354.816 Å		2.77 Å/pix.
x 128 pix.
= 354.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.772 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-4.8783126 - 9.696459000000001
Average (Standard dev.)0.0061186515 (±0.9037787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 354.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45834_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: half2 map

Fileemd_45834_half_map_1.map
Annotationhalf2 map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map

Fileemd_45834_half_map_2.map
Annotationhalf1 map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Ebola virus

EntireName: Ebola virus
Components
  • Virus: Ebola virus - Eckron (Zaire, 1976)

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Supramolecule #1: Ebola virus - Eckron (Zaire, 1976)

SupramoleculeName: Ebola virus - Eckron (Zaire, 1976) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: KZ52 antibody fragment bound to Ebola virus-like particles which contain GP and VP40
NCBI-ID: 129000 / Sci species name: Ebola virus - Eckron (Zaire, 1976) / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.5 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Software - details: relion tomo / Number subtomograms used: 13520
ExtractionNumber tomograms: 18 / Number images used: 130000
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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