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- EMDB-7956: Negative stain EM map of Pan-EBOV antibody 515 Fab in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-7956
TitleNegative stain EM map of Pan-EBOV antibody 515 Fab in complex with EBOV GPdMuc trimer
Map dataNegative stain EM map of Pan-EBOV antibody 515 Fab in complex with EBOV GPdMuc.
Sample
  • Complex: EBOV GPdMuc in complex with Pan-Ebolavirus antibody 515 Fab
    • Complex: EBOV GPdMuc
    • Complex: Pan-Ebolavirus antibody 515 Fab
Biological speciesEbola virus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 13.4 Å
AuthorsWard AB / Turner HL
CitationJournal: Immunity / Year: 2018
Title: Multifunctional Pan-ebolavirus Antibody Recognizes a Site of Broad Vulnerability on the Ebolavirus Glycoprotein.
Authors: Pavlo Gilchuk / Natalia Kuzmina / Philipp A Ilinykh / Kai Huang / Bronwyn M Gunn / Aubrey Bryan / Edgar Davidson / Benjamin J Doranz / Hannah L Turner / Marnie L Fusco / Matthew S Bramble / ...Authors: Pavlo Gilchuk / Natalia Kuzmina / Philipp A Ilinykh / Kai Huang / Bronwyn M Gunn / Aubrey Bryan / Edgar Davidson / Benjamin J Doranz / Hannah L Turner / Marnie L Fusco / Matthew S Bramble / Nicole A Hoff / Elad Binshtein / Nurgun Kose / Andrew I Flyak / Robin Flinko / Chiara Orlandi / Robert Carnahan / Erica H Parrish / Alexander M Sevy / Robin G Bombardi / Prashant K Singh / Patrick Mukadi / Jean Jacques Muyembe-Tamfum / Melanie D Ohi / Erica Ollmann Saphire / George K Lewis / Galit Alter / Andrew B Ward / Anne W Rimoin / Alexander Bukreyev / James E Crowe /
Abstract: Ebolaviruses cause severe disease in humans, and identification of monoclonal antibodies (mAbs) that are effective against multiple ebolaviruses are important for therapeutics development. Here we ...Ebolaviruses cause severe disease in humans, and identification of monoclonal antibodies (mAbs) that are effective against multiple ebolaviruses are important for therapeutics development. Here we describe a distinct class of broadly neutralizing human mAbs with protective capacity against three ebolaviruses infectious for humans: Ebola (EBOV), Sudan (SUDV), and Bundibugyo (BDBV) viruses. We isolated mAbs from human survivors of ebolavirus disease and identified a potent mAb, EBOV-520, which bound to an epitope in the glycoprotein (GP) base region. EBOV-520 efficiently neutralized EBOV, BDBV, and SUDV and also showed protective capacity in relevant animal models of these infections. EBOV-520 mediated protection principally by direct virus neutralization and exhibited multifunctional properties. This study identified a potent naturally occurring mAb and defined key features of the human antibody response that may contribute to broad protection. This multifunctional mAb and related clones are promising candidates for development as broadly protective pan-ebolavirus therapeutic molecules.
History
DepositionMay 29, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseApr 10, 2019-
UpdateApr 10, 2019-
Current statusApr 10, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7956.png

Downloads & links

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Map

FileDownload / File: emd_7956.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of Pan-EBOV antibody 515 Fab in complex with EBOV GPdMuc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 144 pix.
= 295.2 Å		2.05 Å/pix.
x 144 pix.
= 295.2 Å		2.05 Å/pix.
x 144 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0322 / Movie #1: 0.0322
Minimum - Maximum-0.062757835 - 0.13317294
Average (Standard dev.)0.00043091842 (±0.008707412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 295.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z295.200295.200295.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0630.1330.000

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Supplemental data

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Sample components

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Entire : EBOV GPdMuc in complex with Pan-Ebolavirus antibody 515 Fab

EntireName: EBOV GPdMuc in complex with Pan-Ebolavirus antibody 515 Fab
Components
  • Complex: EBOV GPdMuc in complex with Pan-Ebolavirus antibody 515 Fab
    • Complex: EBOV GPdMuc
    • Complex: Pan-Ebolavirus antibody 515 Fab

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Supramolecule #1: EBOV GPdMuc in complex with Pan-Ebolavirus antibody 515 Fab

SupramoleculeName: EBOV GPdMuc in complex with Pan-Ebolavirus antibody 515 Fab
type: complex / ID: 1 / Parent: 0 / Details: Purified through SEC in TBS

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Supramolecule #2: EBOV GPdMuc

SupramoleculeName: EBOV GPdMuc / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Ebola virus
Recombinant expressionOrganism: Drosophila (fruit flies)

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Supramolecule #3: Pan-Ebolavirus antibody 515 Fab

SupramoleculeName: Pan-Ebolavirus antibody 515 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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 / Component - Name: TBS
StainingType: NEGATIVE / Material: Uranyl Formate
GridMaterial: COPPER / Support film - Material: CELLULOSE ACETATE / Support film - topology: HOLEY

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 7086
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION

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