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- EMDB-5413: CryoEM map of the mature astrovirus (HAstV-1) -

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Basic information

Entry
Database: EMDB / ID: 5413
TitleCryoEM map of the mature astrovirus (HAstV-1)
KeywordsT=3 virus
Samplemature human astrovirus HAstV-1
SourceHuman astrovirus / virus
Map dataReconstruction of mature human astrovirus HAstV-1
Methodsingle particle (icosahedral) reconstruction, at 25 A resolution
AuthorsDryden KA / Tihova M / Nowotny N / Matsui SM / Mendez E / Yeager M
CitationJ. Mol. Biol., 2012, 422, 650-658

J. Mol. Biol., 2012, 422, 650-658 StrPapers
Immature and mature human astrovirus: structure, conformational changes, and similarities to hepatitis E virus.
Kelly A Dryden / Mariana Tihova / Norbert Nowotny / Suzanne M Matsui / Ernesto Mendez / Mark Yeager

DateDeposition: Apr 24, 2012 / Header (metadata) release: Jun 28, 2012 / Map release: Jun 28, 2012 / Last update: Apr 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 55
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 55
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
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Slabnear <=> far

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Orientation
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Supplemental images

Downloads & links

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Map

Fileemd_5413.map.gz (map file in CCP4 format, 61772 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
251 pix
2 A/pix
= 502. A
251 pix
2 A/pix
= 502. A
251 pix
2 A/pix
= 502. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2 A
Density
Contour Level:55 (by author), 55 (movie #1):
Minimum - Maximum-189.82514954 - 244.88218689
Average (Standard dev.)6.81235361 (36.43178558)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions251251251
Origin-125-125-125
Limit125125125
Spacing251251251
CellA=B=C: 502 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z222
M x/y/z251251251
origin x/y/z0.0000.0000.000
length x/y/z502.000502.000502.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS251251251
D min/max/mean-189.825244.8826.812

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Supplemental data

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Sample components

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Entire mature human astrovirus HAstV-1

EntireName: mature human astrovirus HAstV-1 / Number of components: 1

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Component #1: virus, Human astrovirus

VirusName: Human astrovirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human astrovirus / 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
Sample solutionBuffer solution: 50mM Tris-HCl, pH 8, 100mM NaCl, 10mM MgCl2, 10mM CaCl2
Support filmholey carbon, glow discharged with amylamine
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: watch drop spread on filter paper before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM120T / Date: Sep 22, 1997
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 35000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1450 - 1850 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: Particles were selected with X3D, and processed with Auto3dem.
Number of projections: 397 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: polar Fourier transform / Software: Auto3dem / Resolution: 25 A / Resolution method: FSC 0.5

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