[English] 日本語
Yorodumi
- EMDB-1920: Improved ab initio 3D reconstruction of the EF-G containing E. co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1920
TitleImproved ab initio 3D reconstruction of the EF-G containing E. coli ribosome by SIMPLE
Map dataThis is a volume of the EF-G containing E. coli ribosome reconstructed by SIMPLE
Sample
  • Sample: EF-G ribosome test data
  • Complex: Ribosome
Keywordsab initio
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM
AuthorsElmlund H
CitationJournal: Ultramicroscopy / Year: 2001
Title: Strul--a method for 3D alignment of single-particle projections based on common line correlation in Fourier space.
Authors: M Lindahl /
Abstract: A central problem of 3D reconstruction in single-particle electron microscopy is the determination of relative orientations of the individual projections contributing to the reconstruction. This ...A central problem of 3D reconstruction in single-particle electron microscopy is the determination of relative orientations of the individual projections contributing to the reconstruction. This article describes an implementation of the method of common lines correlation in Fourier space that allows generation of common lines between an arbitrary number of projections which might posses an arbitrary point group symmetry. Based on this method, it is possible to optimize rotational and translational alignment parameters for individual single-particle projections. The underlying philosophy and details of implementation are discussed, and as an illustration a 3D reconstruction in ice of peroxisomal alcohol oxidase from Pichia pastoris, an octameric assembly with 422-symmetry and a molecular weight of 592 kDa is presented.
History
DepositionJul 2, 2011-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateApr 9, 2014-
Current statusApr 9, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.106
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.106
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1920.png

Downloads & links

-
Map

FileDownload / File: emd_1920.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume of the EF-G containing E. coli ribosome reconstructed by SIMPLE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 128 pix.
= 360.96 Å		2.82 Å/pix.
x 128 pix.
= 360.96 Å		2.82 Å/pix.
x 128 pix.
= 360.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.106 / Movie #1: 0.106
Minimum - Maximum-2.68995261 - 5.58192444
Average (Standard dev.)0.05049846 (±0.28232509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z360.960360.960360.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-2.6905.5820.050

-
Supplemental data

-
Sample components

-
Entire : EF-G ribosome test data

EntireName: EF-G ribosome test data
Components
  • Sample: EF-G ribosome test data
  • Complex: Ribosome

-
Supramolecule #1000: EF-G ribosome test data

SupramoleculeName: EF-G ribosome test data / type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Ribosome

SupramoleculeName: Ribosome / type: complex / ID: 1 / Name.synonym: Ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeOTHER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Software - Name: SIMPLE

+
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