[English] 日本語
- EMDB-1557: Cryo-EM density map of Epsilon-15 bacteriophage icosahedral recon... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1557
TitleCryo-EM density map of Epsilon-15 bacteriophage icosahedral reconstruction from JADAS automatically acquired data at 7.3 Angstrom resolution.
Map dataThis is the density map of the epsilon-15 bacteriophage reconstructed from JADAS automatically acquired images.
SampleEpsilon-15 bacteriophage:
KeywordsSingle-particle / Automated data collection / Reconstruction / Cryo-EM / Epsilon-15 bacteriophage
SourceSalmonella phage epsilon15 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / 7.3 Å resolution
AuthorsZhang J / Nakamura N / Shimizu Y / Liang N / Liu X / Jakana J / Marsh MP / Booth CR / Shinkawa T / Nakata M / Chiu W
CitationJournal: J. Struct. Biol. / Year: 2009
Title: JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.
Authors: Junjie Zhang / Natsuko Nakamura / Yuko Shimizu / Nathan Liang / Xiangan Liu / Joanita Jakana / Michael P Marsh / Christopher R Booth / Takao Shinkawa / Munetaka Nakata / Wah Chiu
DateDeposition: Sep 8, 2008 / Header (metadata) release: Sep 12, 2008 / Map release: Apr 29, 2009 / Last update: Oct 24, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_1557.map.gz (map file in CCP4 format, 182251 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
2.62 Å/pix.
= 943.2 Å
360 pix
2.62 Å/pix.
= 943.2 Å
360 pix
2.62 Å/pix.
= 943.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Contour Level:1.6 (by author), 1.2 (movie #1):
Minimum - Maximum-2.05162 - 4.17608
Average (Standard dev.)0.0414809 (0.320718)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 943.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z943.200943.200943.200
start NX/NY/NZ-81-81-81
MAP C/R/S123
start NC/NR/NS-180-180-180
D min/max/mean-2.0524.1760.041

Supplemental data

Sample components

Entire Epsilon-15 bacteriophage

EntireName: Epsilon-15 bacteriophage
Details: The sample is frozen on carbon support film in vitreous ice.
Number of components: 1
MassTheoretical: 22 MDa / Experimental: 22 MDa

Component #1: virus, Salmonella phage epsilon15

VirusName: Salmonella phage epsilon15 / a.k.a: Epsilon-15 bacteriophage / Class: VIRION
Details: The sample is frozen on carbon support film in vitreous ice.
Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 22 MDa / Experimental: 22 MDa
SpeciesSpecies: Salmonella phage epsilon15 (bacteriophage)
Source (natural)Host Species: Salmonella (bacteria) / Host category: BACTERIA(EUBACTERIA)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Support film400 mesh copper grid with holy carbon film
VitrificationInstrument: NONE / Cryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Details: Data is automatically collected using JEOL Automated Data Acquisition System (JADAS). Microscope used JEM3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (nominal), 56680 X (calibrated) / Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Energy filter: JEOL in-column omega filter
Specimen HolderHolder: JEM3200FSC cryoholder / Model: OTHER / Temperature: 100 K
CameraDetector: GENERIC GATAN (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 181 / Sampling size: 2.62 microns / Bit depth: 8

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7543 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Cross-common lines / Software: Multi-path simulated annealing / CTF correction: Each CCD image / Resolution: 7.3 Å
Resolution method: FSC at 0.5 with our previously published data

About Yorodumi


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

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

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


Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more