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- EMDB-8630: Ebola GP spike in situ in viral membrane -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-8630
TitleEbola GP spike in situ in viral membrane
Map dataEbola GP spike in situ in viral envelope
SampleEbola GP spike != Ebola virus

Ebola GP spike

  • Virus: Ebola virus
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / membrane => GO:0016020 / extracellular region / GP
Function and homology information
Biological speciesEbola virus
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsBooth TF / Beniac DR
CitationJournal: Sci Rep / Year: 2017
Title: Structure of the Ebola virus glycoprotein spike within the virion envelope at 11 Å resolution.
Authors: Daniel R Beniac / Timothy F Booth /
Abstract: We present the structure of the surface Ebola virus (EBOV) trimeric glycoprotein (GP) spike at 11 Å resolution, in situ within the viral plasma membrane of purified virus particles. GP functions ...We present the structure of the surface Ebola virus (EBOV) trimeric glycoprotein (GP) spike at 11 Å resolution, in situ within the viral plasma membrane of purified virus particles. GP functions in cellular attachment, endosomal entry, and membrane fusion to initiate infection, and is a key therapeutic target. Nevertheless, only about half of the GP molecule has yet been solved to atomic resolution, excluding the mucin-like and transmembrane domains, and some of the glycans. Fitting of the atomic resolution X-ray data from expressed, truncated deletion constructs within our 11 Å structure of the entire molecule demonstrates the relationship between the GP1-GP2 domains, the mucin-like and transmembrane domains, and the bilaminar lipid envelope. We show that the mucin-like domain covers the glycan cap and partially occludes the receptor binding sites prior to proteolytic cleavage. Our structure is also consistent with key antibody neutralisation sites on GP being accessible prior to proteolysis. Based on the findings of us and others, GP-mediated binding may create an angle of 18 degrees between the planes of viral and endosomal membranes.
History
DepositionFeb 28, 2017-
Header (metadata) releaseApr 26, 2017-
Map releaseApr 26, 2017-
UpdateApr 26, 2017-
Current statusApr 26, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00232
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00232
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8630.png

Downloads & links

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Map

FileDownload / File: emd_8630.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEbola GP spike in situ in viral envelope
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.15 Å/pix.
x 150 pix.
= 322.5 Å		2.15 Å/pix.
x 150 pix.
= 322.5 Å		2.15 Å/pix.
x 150 pix.
= 322.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.00232 / Movie #1: 0.00232
Minimum - Maximum-0.019076252 - 0.038811773
Average (Standard dev.)-0.000029971377 (±0.0020102025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 322.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.152.152.15
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z322.500322.500322.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0190.039-0.000

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Supplemental data

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Sample components

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Entire : Ebola GP spike

EntireName: Ebola GP spike
Components
  • Virus: Ebola virus

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Supramolecule #1: Ebola virus

SupramoleculeName: Ebola virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1570291 / Sci species name: Ebola virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 10.0 e/Å2

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32960

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