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- EMDB-3303: Cryo-EM reconstruction of Seneca VAlley Virus - receptor complex -

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Basic information

Entry
Database: EMDB / ID: 3303
TitleCryo-EM reconstruction of Seneca VAlley Virus - receptor complex
SampleCryo-EM reconstruction of Seneca Valley Virus - receptor complex
SourceSeneca valley virus / virus
Map dataCryo-EM reconstruction of SVV-receptor complex
Methodsingle particle (icosahedral) reconstruction, at 18 Å resolution
AuthorsMiles LA / Burga L / Bostina M / Poirier JT / Rudin CM
CitationJ. Clin. Invest., 2017, 127, 2957-2967

J. Clin. Invest., 2017, 127, 2957-2967 Yorodumi Papers
Anthrax toxin receptor 1 is the cellular receptor for Seneca Valley virus.
Linde A Miles / Laura N Burga / Eric E Gardner / Mihnea Bostina / John T Poirier / Charles M Rudin

DateDeposition: Jan 21, 2016 / Header (metadata) release: Feb 3, 2016 / Map release: Oct 11, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3303.map.gz (map file in CCP4 format, 22783 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
3.12 Å/pix.
= 561.6 Å
180 pix
3.12 Å/pix.
= 561.6 Å
180 pix
3.12 Å/pix.
= 561.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.12 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.00622528 - 0.13083661
Average (Standard dev.)0.00792713 (0.02601571)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin383838
Limit217217217
Spacing180180180
CellA=B=C: 561.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.123.123.12
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z561.600561.600561.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS383838
NC/NR/NS180180180
D min/max/mean-0.0060.1310.008

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Supplemental data

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Sample components

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Entire Cryo-EM reconstruction of Seneca Valley Virus - receptor complex

EntireName: Cryo-EM reconstruction of Seneca Valley Virus - receptor complex
Number of components: 2

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Component #1: virus, Seneca valley virus

VirusName: Seneca valley virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Seneca valley virus / virus
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: LEICA KF80 / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Oct 1, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: JEOL
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 400

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 400
3D reconstructionSoftware: Relion / Resolution: 18 Å / Resolution method: FSC 0.143, gold-standard

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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