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- EMDB-7923: VIC101 Fab in complex with Ebola virus GP -

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Basic information

Entry
Database: EMDB / ID: 7923
TitleVIC101 Fab in complex with Ebola virus GP
Map dataVIC101 antibody Fab in complex with Ebola virus GP
SampleComplex of VIC101 Fab bound to Ebola virus GP:
SourceEbola virus - Mayinga, Zaire, 1976
Methodsingle particle reconstruction / negative staining / 22 Å resolution
AuthorsTurner H / Murin CD / Pallesen J / Ward AB
CitationJournal: to be published
Title: Systematic analysis of monoclonal antibodies against Ebola virus GP defines features that contribute to protection
Authors: Saphire EO / Schendel SL / Fusco ML / Gangavarapu K / Gunn BM / Wec AZ / Halfmann PJ / Brannan JM / Herbert AS / Qiu X / Wagh K / He S / Giorgi EE / Theiler J / Pommert KBJ / Turner HL / Murin CD / Pallesen J / Davidson E / Ahmed R / Aman MJ / Bukreyev A / Burton DR / Crowe Jr. JE / Georgiou G / Krammer F / Kyratsous CA / Lai J / Nykiforuk C / Takada A / Townsend AR / Volchkov V / Walker LM / Wang C / Zeitlin L / Doranz BJ / Ward AB / Korber B / Kobinger GP / Andersen KG / Kawaoka Y / Alter G / Chandran K / Dye JM
DateDeposition: May 24, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Jul 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7923.map.gz (map file in CCP4 format, 2049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
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:4.45 (by author), 4.45 (movie #1):
Minimum - Maximum-6.6838913 - 17.262587
Average (Standard dev.)0.01648663 (0.97504973)
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-6.68417.2630.016

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Supplemental data

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Sample components

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Entire Complex of VIC101 Fab bound to Ebola virus GP

EntireName: Complex of VIC101 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 VIC101 Fab bound to Ebola virus GP

ProteinName: Complex of VIC101 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: 59

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 6752
3D reconstructionResolution: 22 Å / Resolution method: FSC 0.5 CUT-OFF

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