[English] 日本語
Yorodumi
- EMDB-5204: Average of 50 Epsilon15 subtomograms using electron cryo-tomography -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5204
TitleAverage of 50 Epsilon15 subtomograms using electron cryo-tomography
Map dataThis is an image of a surface rendered top-view of Epsilon15
Sample
  • Sample: Epsilon15
  • Virus: epsilon15 (virus)
KeywordsElectron tomography / Phase plate / Bacteriophage
Biological speciesepsilon15 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 38.0 Å
AuthorsMurata K / Liu X / Danev R / Jakana J / Schmid MF / King J / Nagayama K / Chiu W
CitationJournal: Structure / Year: 2010
Title: Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions.
Authors: Kazuyoshi Murata / Xiangan Liu / Radostin Danev / Joanita Jakana / Michael F Schmid / Jonathan King / Kuniaki Nagayama / Wah Chiu /
Abstract: Zernike phase contrast cryo-electron microscopy (ZPC-cryoEM) is an emerging technique that is capable of producing higher image contrast than conventional cryoEM. By combining this technique with ...Zernike phase contrast cryo-electron microscopy (ZPC-cryoEM) is an emerging technique that is capable of producing higher image contrast than conventional cryoEM. By combining this technique with advanced image processing methods, we achieved subnanometer resolution for two biological specimens: 2D bacteriorhodopsin crystal and epsilon15 bacteriophage. For an asymmetric reconstruction of epsilon15 bacteriophage, ZPC-cryoEM can reduce the required amount of data by a factor of approximately 3, compared with conventional cryoEM. The reconstruction was carried out to 13 A resolution without the need to correct the contrast transfer function. New structural features at the portal vertex of the epsilon15 bacteriophage are revealed in this reconstruction. Using ZPC cryo-electron tomography (ZPC-cryoET), a similar level of data reduction and higher resolution structures of epsilon15 bacteriophage can be obtained relative to conventional cryoET. These results show quantitatively the benefits of ZPC-cryoEM and ZPC-cryoET for structural determinations of macromolecular machines at nanometer and subnanometer resolutions.
History
DepositionJun 30, 2010-
Header (metadata) releaseSep 1, 2010-
Map releaseSep 1, 2010-
UpdateJul 8, 2011-
Current statusJul 8, 2011Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5204_1.png

Downloads & links

-
Map

FileDownload / File: emd_5204.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered top-view of Epsilon15
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.88 Å/pix.
x 216 pix.
= 1054.08 Å		4.88 Å/pix.
x 216 pix.
= 1054.08 Å		4.88 Å/pix.
x 216 pix.
= 1054.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-2.66289 - 5.11135
Average (Standard dev.)0.0795056 (±0.424669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 1054.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.884.884.88
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z1054.0801054.0801054.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-2.6635.1110.080

-
Supplemental data

-
Sample components

-
Entire : Epsilon15

EntireName: Epsilon15 (virus)
Components
  • Sample: Epsilon15
  • Virus: epsilon15 (virus)

-
Supramolecule #1000: Epsilon15

SupramoleculeName: Epsilon15 / type: sample / ID: 1000 / Details: The samples was monodisperse / Number unique components: 6
Molecular weightTheoretical: 500 KDa

-
Supramolecule #1: epsilon15

SupramoleculeName: epsilon15 / type: virus / ID: 1 / Name.synonym: bacteriophage / Sci species name: epsilon15 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage
Host (natural)Organism: Salmonella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 700 Å / T number (triangulation number): 7

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 10 mM Tris pH7.5, 25 mM NaCl and 5 mM MgCl2
GridDetails: Quantifoil R2/2 grid
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: Blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeJEOL 2200FS
TemperatureAverage: 90 K
Specialist opticsEnergy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsWeak beam illumination
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 15 µm / Number real images: 71 / Average electron dose: 80 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.3 mm / Nominal magnification: 20000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °

-
Image processing

DetailsAverage number of projections used in the 3D reconstructions: 50.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD
Details: Final maps were calculated from fifty averaged datasets

+
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