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CryoEM map of the mature astrovirus (HAstV-1)

by single particle (icosahedral) reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 55, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 55, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5413
TitleCryoEM map of the mature astrovirus (HAstV-1)
MapReconstruction of mature human astrovirus HAstV-1
Samplemature human astrovirus HAstV-1
KeywordsT=3 virus
AuthorsDryden KA, Tihova M, Nowotny N, Matsui SM, Mendez E, Yeager M
DateDeposition: 2012-04-24, Header release: 2012-06-28, Map release: 2012-06-28, Last update: 2012-11-07
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 55, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 55, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 422, Issue 5, Page 650-8, Year 2012
TitleImmature and mature human astrovirus: structure, conformational changes, and similarities to hepatitis E virus.
AuthorsKelly A Dryden, Mariana Tihova, Norbert Nowotny, Suzanne M Matsui, Ernesto Mendez, Mark Yeager
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
KeywordsAmino Acid Sequence, Cryoelectron Microscopy, Hepatitis E virus (ultrastructure), Humans, Image Processing, Computer-Assisted, Mamastrovirus (ultrastructure), Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA, Virion (ultrastructure)
LinksPII: S0022-2836(12)00502-5, DOI: 10.1016/j.jmb.2012.06.029, PubMed: 22743104
Map
Fileemd_5413.map.gz ( map file in CCP4 format, 61772 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:55 (by author), 55 (movie #1):
Minimum - Maximum: -189.82514954 - 244.88218689
Average (Standard dev.): 6.81235361 (36.43178558)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions251251251
Origin-125-125-125
Limit125125125
Spacing251251251
Unit CellA= B= C: 502 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-189.825244.8826.812
Annotation DetailsReconstruction of mature human astrovirus HAstV-1
Supplement
Images
Images
Sample
Namemature human astrovirus HAstV-1
Number of Components1
Component #1: virus - Human astrovirus
Scientific nameHuman astrovirus
Scientific Name of SpeciesHuman astrovirus
NCBI taxonomy12702
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 9606
Host Species: Homo sapiens
Host Category: VERTEBRATES
ShellID: 1 , Diameter: 440 A, T Number: 3
Experiment
Sample Preparation
Specimen Support Detailsholey carbon, glow discharged with amylamine
Specimen Stateparticle
BufferDetails: 50mM Tris-HCl, pH 8, 100mM NaCl, 10mM MgCl2, 10mM CaCl2
Vitrification
Methodwatch drop spread on filter paper before plunging
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
Imaging
MicroscopeFEI/PHILIPS CM120T
Date22-SEP-1997
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 35000
Imaging ModeBRIGHT FIELD
Defocus1450 nm - 1850 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerZEISS SCAI
Number of Digital Images6
Sampling Size7
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmpolar Fourier transform
SoftwareAuto3dem
Resolution By Author25 A
Resolution MethodFSC 0.5
Single Particle
DetailsParticles were selected with X3D, and processed with Auto3dem.
Number of Projections397
Applied SymmetryI (icosahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5413.xml (6.5 KB)
Map dataemd_5413.map.gz (22.3 MB)
Imagesemd_5413_1.jpg (58.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5413
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.2 KB