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- EMDB-6004: Cryo-electron tomography of glycoprotein lacking the mucin-like d... -

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Basic information

Entry
Database: EMDB / ID: EMD-6004
TitleCryo-electron tomography of glycoprotein lacking the mucin-like domain from Ebola virus-like particles
Map dataMolecular structure of Ebola VLP glycoprotein trimer lacking the mucin-like domain
Sample
  • Sample: Molecular structure of Ebola VLP glycoprotein trimer lacking the mucin-like domain
  • Protein or peptide: Envelope glycoprotein
KeywordsEbola / glycoprotein / mucin-like domain
Biological speciesZaire ebolavirus
Methodsubtomogram averaging / cryo EM
AuthorsTran EEH / Simmons JA / Bartesaghi A / Shoemaker CJ / Nelson E / White JM / Subramaniam S
CitationJournal: J Virol / Year: 2014
Title: Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography.
Authors: Erin E H Tran / James A Simmons / Alberto Bartesaghi / Charles J Shoemaker / Elizabeth Nelson / Judith M White / Sriram Subramaniam /
Abstract: The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three- ...The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three-dimensional structure for the full-length glycoprotein in a near-native state and compared it to that of a glycoprotein lacking the MLD. Our results, which show that the MLD is located at the apex and the sides of each glycoprotein monomer, provide a structural template for analysis of MLD function.
History
DepositionJul 29, 2014-
Header (metadata) releaseAug 6, 2014-
Map releaseAug 6, 2014-
UpdateSep 3, 2014-
Current statusSep 3, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.179
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.179
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6004.png

Downloads & links

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Map

FileDownload / File: emd_6004.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMolecular structure of Ebola VLP glycoprotein trimer lacking the mucin-like domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 99 pix.
= 405.9 Å		4.1 Å/pix.
x 55 pix.
= 225.5 Å		4.1 Å/pix.
x 55 pix.
= 225.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.179 / Movie #1: 0.179
Minimum - Maximum-0.65826869 - 1.11070156
Average (Standard dev.)-0.0025089 (±0.11215557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions555599
Spacing555599
CellA: 225.5 Å / B: 225.5 Å / C: 405.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z555599
origin x/y/z0.0000.0000.000
length x/y/z225.500225.500405.900
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS555599
D min/max/mean-0.6581.111-0.003

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Supplemental data

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Sample components

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Entire : Molecular structure of Ebola VLP glycoprotein trimer lacking the ...

EntireName: Molecular structure of Ebola VLP glycoprotein trimer lacking the mucin-like domain
Components
  • Sample: Molecular structure of Ebola VLP glycoprotein trimer lacking the mucin-like domain
  • Protein or peptide: Envelope glycoprotein

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Supramolecule #1000: Molecular structure of Ebola VLP glycoprotein trimer lacking the ...

SupramoleculeName: Molecular structure of Ebola VLP glycoprotein trimer lacking the mucin-like domain
type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 1

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Macromolecule #1: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 1
Details: Envelope glycoproteins present on the surface of virus-like particles
Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Zaire ebolavirus / synonym: Ebola
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T
Recombinant plasmid: pVP40, pBeta-Lactamase-VP40, pmCherry-VP40, pEbola Zaire GPdelta mucin

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 130 mM NaCl, 20 mM HEPES, 10% sucrose
GridDetails: 200 mesh Quantifoil Multi-A
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK IV
Method: Blot for 4 seconds at 22 degrees C, 100% humidity, blot force 4, plunge into an ethane slurry cooled by liquid nitrogen.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 81 K
Specialist opticsEnergy filter - Name: GATAN GIF / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateMay 16, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 29 / Average electron dose: 150 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 34000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsSubtomogram density was selected using an automatic selection program.
Final reconstructionSoftware - Name: IMOD / Number subtomograms used: 6304

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Atomic model buiding 1

Initial modelPDB ID:

3csy


Chain - #0 - Chain ID: I / Chain - #1 - Chain ID: K / Chain - #2 - Chain ID: M / Chain - #3 - Chain ID: O
SoftwareName: Chimera
DetailsProtocol: rigid body, automated fitting procedures
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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