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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-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.
Sample
  • Sample: Epsilon-15 bacteriophage
  • Virus: Salmonella phage epsilon15 (virus)
KeywordsSingle-particle / Automated data collection / Reconstruction / Cryo-EM / Epsilon-15 bacteriophage
Biological speciesSalmonella phage epsilon15 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
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 /
Abstract: The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate ...The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate image acquisition for ice-embedded single particles under low dose conditions. Its built-in flexibility permits users to customize the order of various imaging operations. In this paper, we describe how JADAS is used to accurately locate and image suitable specimen areas on a grid of ice-embedded particles. We also demonstrate the utility of JADAS by imaging the epsilon 15 bacteriophage with the JEM3200FSC electron cryo-microscope, showing that sufficient images can be collected in a single 8h session to yield a subnanometer resolution structure which agrees with the previously determined structure.
History
DepositionSep 8, 2008-
Header (metadata) releaseSep 12, 2008-
Map releaseApr 29, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

1557.jpg

Downloads & links

-
Map

FileDownload / File: emd_1557.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map of the epsilon-15 bacteriophage reconstructed from JADAS automatically acquired images.
Voxel sizeX=Y=Z: 2.62 Å
Density
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.2
Minimum - Maximum-2.05162 - 4.17608
Average (Standard dev.)0.0414809 (±0.320718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 943.2 Å
α=β=γ: 90 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-2.0524.1760.041

-
Supplemental data

-
Sample components

-
Entire : Epsilon-15 bacteriophage

EntireName: Epsilon-15 bacteriophage
Components
  • Sample: Epsilon-15 bacteriophage
  • Virus: Salmonella phage epsilon15 (virus)

-
Supramolecule #1000: Epsilon-15 bacteriophage

SupramoleculeName: Epsilon-15 bacteriophage / type: sample / ID: 1000
Details: The sample is frozen on carbon support film in vitreous ice.
Number unique components: 1
Molecular weightExperimental: 22 MDa / Theoretical: 22 MDa

-
Supramolecule #1: Salmonella phage epsilon15

SupramoleculeName: Salmonella phage epsilon15 / type: virus / ID: 1 / Name.synonym: Epsilon-15 bacteriophage
Details: The sample is frozen on carbon support film in vitreous ice.
NCBI-ID: 215158 / Sci species name: Salmonella phage epsilon15 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Epsilon-15 bacteriophage
Host (natural)Organism: Salmonella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 22 MDa / Theoretical: 22 MDa
Virus shellShell ID: 1 / T number (triangulation number): 7

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

GridDetails: 400 mesh copper grid with holy carbon film
VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal magnification: 40000
Specialist opticsEnergy filter - Name: JEOL in-column omega filter
Sample stageSpecimen holder: JEM3200FSC cryoholder / Specimen holder model: OTHER
TemperatureAverage: 100 K
DetailsData is automatically collected using JEOL Automated Data Acquisition System (JADAS). Microscope used JEM3200FSC
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 2.62 µm / Number real images: 181 / Average electron dose: 20 e/Å2 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: Each CCD image
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: OTHER / Software - Name: Multi-path simulated annealing / Number images used: 7543

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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