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- EMDB-7915: VIC163 Fab in complex with Ebola virus GP -

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Basic information

Entry
Database: EMDB / ID: EMD-7915
TitleVIC163 Fab in complex with Ebola virus GP
Map dataVIC163 antibody Fab in complex with Ebola virus GP
Sample
  • Complex: Complex of VIC163 Fab bound to Ebola virus GP
Biological speciesEbola virus - Mayinga, Zaire, 1976
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
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 / ...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.
History
DepositionMay 24, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseJul 25, 2018-
UpdateSep 12, 2018-
Current statusSep 12, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 19
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 19
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7915.png

Downloads & links

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Map

FileDownload / File: emd_7915.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVIC163 antibody Fab in complex with Ebola virus GP
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 19. / Movie #1: 19
Minimum - Maximum-29.189392000000002 - 77.024959999999993
Average (Standard dev.)0.3663797 (±4.592435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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-69-50-137
NX/NY/NZ136114193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-29.18977.0250.366

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Supplemental data

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Sample components

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Entire : Complex of VIC163 Fab bound to Ebola virus GP

EntireName: Complex of VIC163 Fab bound to Ebola virus GP
Components
  • Complex: Complex of VIC163 Fab bound to Ebola virus GP

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Supramolecule #1: Complex of VIC163 Fab bound to Ebola virus GP

SupramoleculeName: Complex of VIC163 Fab bound to Ebola virus GP / type: complex / ID: 1 / Parent: 0
Details: Fab fragment generated by proteolytic cleavage of IgG antibody with papain.
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2 / Recombinant plasmid: pMT-puro

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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
20.0 mMTrisTris(hydroxymethyl)aminomethane

Details: Solution was made from 10X concentration.
StainingType: NEGATIVE / Material: uranyl formate / Details: Stained using 2% UF on carbon coated grids.
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 100 / Average exposure time: 0.7 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 0.001 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Common lines model.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 10556
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN2
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN2

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