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- EMDB-5414: CryoEM map of the immature human astrovirus HAstV-8 -

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Basic information

Entry
Database: EMDB / ID: EMD-5414
TitleCryoEM map of the immature human astrovirus HAstV-8
Map data
Sampleimmature human astrovirus HAstV-8:
virus
KeywordsT=3 virus
Biological speciesHuman astrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 25 Å
AuthorsDryden KA / Tihova M / Nowotny N / Matsui SM / Mendez E / Yeager M
CitationJournal: J Mol Biol / Year: 2012
Title: Immature and mature human astrovirus: structure, conformational changes, and similarities to hepatitis E virus.
Authors: Kelly A Dryden / Mariana Tihova / Norbert Nowotny / Suzanne M Matsui / Ernesto Mendez / Mark Yeager /
Abstract: Human astroviruses (HAstVs) are a major cause of gastroenteritis. HAstV assembles from the structural protein VP90 and undergoes a cascade of proteolytic cleavages. Cleavage to VP70 is required for ...Human astroviruses (HAstVs) are a major cause of gastroenteritis. HAstV assembles from the structural protein VP90 and undergoes a cascade of proteolytic cleavages. Cleavage to VP70 is required for release of immature particles from cells, and subsequent cleavage by trypsin confers infectivity. We used electron cryomicroscopy and icosahedral image analysis to determine the first experimentally derived, three-dimensional structures of an immature VP70 virion and a fully proteolyzed, infectious virion. Both particles display T=3 icosahedral symmetry and nearly identical solid capsid shells with diameters of ~350Å. Globular spikes emanate from the capsid surface, yielding an overall diameter of ~440Å. While the immature particles display 90 dimeric spikes, the mature capsid only displays 30 spikes, located on the icosahedral 2-fold axes. Loss of the 60 peripentonal spikes likely plays an important role in viral infectivity. In addition, immature HAstV bears a striking resemblance to the structure of hepatitis E virus (HEV)-like particles, as previously predicted from structural similarity of the crystal structure of the astrovirus spike domain with the HEV P-domain [Dong, J., Dong, L., Méndez, E. & Tao, Y. (2011). Crystal structure of the human astrovirus capsid spike. Proc. Natl. Acad. Sci. USA108, 12681-12686]. Similarities between their capsid shells and dimeric spikes and between the sequences of their capsid proteins suggest that these viral families are phylogenetically related and may share common assembly and activation mechanisms.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionApr 24, 2012-
Header (metadata) releaseJun 28, 2012-
Map releaseJun 28, 2012-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.85
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.85
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5414.map.gz / Format: CCP4 / Size: 147.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 341 pix.
= 531.96 Å
1.56 Å/pix.
x 341 pix.
= 531.96 Å
1.56 Å/pix.
x 341 pix.
= 531.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density
Contour LevelBy AUTHOR: 0.85 / Movie #1: 0.85
Minimum - Maximum-4.179986 - 3.50760221
Average (Standard dev.)0.15266505 (±0.67520535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions341341341
Spacing341341341
CellA=B=C: 531.95996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.561.561.56
M x/y/z341341341
origin x/y/z0.0000.0000.000
length x/y/z531.960531.960531.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS341341341
D min/max/mean-4.1803.5080.153

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Supplemental data

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Sample components

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Entire immature human astrovirus HAstV-8

EntireName: immature human astrovirus HAstV-8 / 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
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 50mM Tris-HCl, pH 7.4, 100mM NaCl, 10mM EDTA
Support filmglow 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: Dec 22, 2003
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 45000 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: 7 / Scanner: ZEISS SCAI / Sampling size: 7 µm

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Image processing

ProcessingMethod: single particle reconstruction
Details: Particles were boxed with X3D and processed with Auto3dem
Number of projections: 451 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: polar Fourier transform / Software: Auto3dem / Resolution: 25 Å / Resolution method: FSC 0.5

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