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- EMDB-7934: VIC130 Fab in complex with Ebola virus GP -

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Basic information

Entry
Database: EMDB / ID: 7934
TitleVIC130 Fab in complex with Ebola virus GP
Map dataVIC130 antibody Fab in complex with Ebola virus GP
SampleComplex of VIC130 Fab bound to Ebola virus GP:
SourceEbola virus - Mayinga, Zaire, 1976
Methodsingle particle reconstruction / negative staining / 26 Å resolution
AuthorsTurner H / Murin CD / Pallesen J / Ward AB
CitationJournal: Cell / Year: 2018
Title: Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection.
Authors: Erica Ollmann Saphire / Sharon L Schendel / Marnie L Fusco / Karthik Gangavarapu / Bronwyn M Gunn / Anna Z Wec / Peter J Halfmann / Jennifer M Brannan / Andrew S Herbert / Xiangguo Qiu / Kshitij Wagh / Shihua He / Elena E Giorgi / James Theiler / Kathleen B J Pommert / Tyler B Krause / Hannah L Turner / Charles D Murin / Jesper Pallesen / Edgar Davidson / Rafi Ahmed / M Javad Aman / Alexander Bukreyev / Dennis R Burton / James E Crowe / Carl W Davis / George Georgiou / Florian Krammer / Christos A Kyratsous / Jonathan R Lai / Cory Nykiforuk / Michael H Pauly / Pramila Rijal / Ayato Takada / Alain R Townsend / Viktor Volchkov / Laura M Walker / Cheng-I Wang / Larry Zeitlin / Benjamin J Doranz / Andrew B Ward / Bette Korber / Gary P Kobinger / Kristian G Andersen / Yoshihiro Kawaoka / Galit Alter / Kartik Chandran / John M Dye /
Abstract: Antibodies are promising post-exposure therapies against emerging viruses, but which antibody features and in vitro assays best forecast protection are unclear. Our international consortium ...Antibodies are promising post-exposure therapies against emerging viruses, but which antibody features and in vitro assays best forecast protection are unclear. Our international consortium systematically evaluated antibodies against Ebola virus (EBOV) using multidisciplinary assays. For each antibody, we evaluated epitopes recognized on the viral surface glycoprotein (GP) and secreted glycoprotein (sGP), readouts of multiple neutralization assays, fraction of virions left un-neutralized, glycan structures, phagocytic and natural killer cell functions elicited, and in vivo protection in a mouse challenge model. Neutralization and induction of multiple immune effector functions (IEFs) correlated most strongly with protection. Neutralization predominantly occurred via epitopes maintained on endosomally cleaved GP, whereas maximal IEF mapped to epitopes farthest from the viral membrane. Unexpectedly, sGP cross-reactivity did not significantly influence in vivo protection. This comprehensive dataset provides a rubric to evaluate novel antibodies and vaccine responses and a roadmap for therapeutic development for EBOV and related viruses.
DateDeposition: May 24, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Aug 22, 2018

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Structure visualization

Movie
  • Surface view colored by cylindrical radius
  • Surface level: 22
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 22
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_7934.map.gz (map file in CCP4 format, 2049 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
4.1 Å/pix.
= 328. Å
80 pix
4.1 Å/pix.
= 328. Å
80 pix
4.1 Å/pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density
Contour Level:22.0 (by author), 22 (movie #1):
Minimum - Maximum-61.783431999999998 - 86.830510000000004
Average (Standard dev.)0.42454782 (5.4936633)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40.-40.-40.
Limit39.39.39.
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-61.78386.8310.425

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Supplemental data

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Sample components

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Entire Complex of VIC130 Fab bound to Ebola virus GP

EntireName: Complex of VIC130 Fab bound to Ebola virus GP
Details: Fab fragment generated by proteolytic cleavage of IgG antibody with papain.
Number of components: 1

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Component #1: protein, Complex of VIC130 Fab bound to Ebola virus GP

ProteinName: Complex of VIC130 Fab bound to Ebola virus GP
Details: Fab fragment generated by proteolytic cleavage of IgG antibody with papain.
Recombinant expression: No
SourceSpecies: Ebola virus - Mayinga, Zaire, 1976
Source (engineered)Expression System: Drosophila melanogaster (fruit fly) / Vector: pMT-puro / Cell of expression system: S2

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.02 mg/ml / Buffer solution: Solution was made from 10X concentration. / pH: 7.4
StainingStained using 2% UF on carbon coated grids.
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 52000. X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 1.0 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 97

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 10551
3D reconstructionResolution: 26 Å / Resolution method: FSC 0.5 CUT-OFF

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