[English] 日本語
Yorodumi
- EMDB-5413: CryoEM map of the mature astrovirus (HAstV-1) -

+
Open data


ID or keywords:

Loading...

no data

-
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 Å 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: Nov 7, 2012

-
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
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

emd_5413_1.jpg

Downloads & links

-
Map

Fileemd_5413.map.gz (map file in CCP4 format, 61772 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
251 pix
2 Å/pix.
= 502. Å		251 pix
2 Å/pix.
= 502. Å		251 pix
2 Å/pix.
= 502. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
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 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z251251251
origin x/y/z0.0000.0000.000
length x/y/z502.000502.000502.000
α/β/γ90.00090.00090.000
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

-
Supplemental data

-
Sample components

-
Entire mature human astrovirus HAstV-1

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

-
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

-
Experimental details

-
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

-
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

-
Image acquisition

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

-
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 Å / Resolution method: FSC 0.5

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more