[English] 日本語
Yorodumi
- EMDB-5172: 3.6 Angstrom cryoEM structure of human adenovirus type 5 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5172
Title3.6 Angstrom cryoEM structure of human adenovirus type 5
Keywordshuman adenovirus / cryoEM / 3D reconstruction / full-atom model / interaction network
Samplehuman adenovirus type 5
SourceHuman adenovirus 5 / virus / human adenovirus type 5
Map dataThe cryoEM density map is for a huge virus (920A in diameter)and the size is 2.4GB.
Methodsingle particle (icosahedral) reconstruction, at 3.6 A resolution
AuthorsLiu H / Jin L / Koh SBS / Atanasov I / Schein S / Wu L / Zhou ZH
CitationScience, 2010, 329, 1038-1043

Science, 2010, 329, 1038-1043 StrPapers
Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks.
Hongrong Liu / Lei Jin / Sok Boon S Koh / Ivo Atanasov / Stan Schein / Lily Wu / Z Hong Zhou

DateDeposition: Mar 9, 2010 / Header (metadata) release: May 21, 2010 / Map release: Sep 1, 2010 / Last update: Mar 9, 2010

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3iyn
  • Surface level: 8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3izo
  • Surface level: 8
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

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

Downloads & links

-
Map

Fileemd_5172.map.gz (map file in CCP4 format, 1242298 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
430 pix
1.1 A/pix
= 473. A
860 pix
1.1 A/pix
= 946. A
860 pix
1.1 A/pix
= 946. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.1 A
Density
Contour Level:8 (by author), 8 (movie #1):
Minimum - Maximum-37.9406 - 48.2722
Average (Standard dev.)0.132958 (3.9127)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions860860430
Origin-430-4300
Limit429429429
Spacing860860430
CellA: 946 A / B: 946 A / C: 473 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.11.11.1
M x/y/z860860430
origin x/y/z0.0000.0000.000
length x/y/z946.000946.000473.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-430-4300
NC/NR/NS860860430
D min/max/mean-37.94148.2720.133

-
Supplemental data

-
Sample components

-
Entire human adenovirus type 5

EntireName: human adenovirus type 5
Details: E1B gene-attenuated oncolytic human adenovirus type 5 was propagated in HEK 293 cells, harvested and liberated by 3 cycles of freezing-thawing and purified by CsCl step gradient ultra-centrifugation. The virion particles were then dialyzed and resuspended in 10 mM Tris (pH 7.5), 1 mM MgCl2.
Number of components: 15 / Oligomeric State: Icosahedral particle

-
Component #1: virus, Human adenovirus 5

VirusName: Human adenovirus 5 / a.k.a: human adenovirus type 5 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
MassTheoretical: 150 MDa / Experimental: 150 MDa
SpeciesSpecies: Human adenovirus 5 / virus / human adenovirus type 5
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 10mM Tris-HCL,1mM MgCl2 / pH: 7.5
Support film200 mesh holey carbon grid
StainingThe virus particles were not stained.
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging
Details: Vitrification instrument: FEI Vitrobot. Vitrification carried out in a chamber with controlled humidity.

-
Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS / Date: May 1, 2009 / Details: low-dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 90 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 756 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8

-
Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: 756 micrographs that clearly showed signals up to 4 Angstrom in their power spectra were selected. Individual particle images (1024 pixel by 1024 pixel) were first boxed out automatically by the autoBox program in the IMIRS package, followed by manual screening with the EMAN boxer program to keep only the well-separated, contamination-free and intact 45000 particles. The program CTFFIND was used to determine the defocus value and astigmatism parameters for each micrograph. Determination of particle orientation and centre, and subsequent 3D reconstruction were done with the IMIRS package, enhanced by icosahedral symmetry-adapted functions.
Number of projections: 31815 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: common lines / Software: IMIRS / CTF correction: Each particle
Details: The program CTFFIND was used to determine the defocus value and astigmatism parameters for each micrograph. We determined particle orientation, centre parameters and subsequent 3D reconstruction with the IMIRS package, enhanced by icosahedral symmetry-adapted functions for 3D reconstruction. We incorporated astigmatism in the CTF correction in both orientation-centre refinement and 3D reconstruction steps. The IMIRS procedure was optimized, and the data processing was completed within two months by three personal computers, each with eight 2.33GHz CPUs and 16G memory.
Resolution: 3.6 A / Resolution method: FSC 0.5

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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