[English] 日本語
Yorodumi
- EMDB-5340: Processed map of GroEL obtained with a CCD camera to compare resu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5340
TitleProcessed map of GroEL obtained with a CCD camera to compare results from cryo SPA with a DDD camera using the same grid. Initial evaluation of a Direct Detection Device detector for single particle cryo-electron microscopy.
Map dataAmplitude corrected and filtered GroEL map
Sample
  • Sample: GroEL
  • Protein or peptide: GroEL
KeywordsGroEL
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsMilazzo AC / Cheng A / Moeller A / Lyumkis D / Jacovetty E / Polukas J / Ellisman MH / Xuong NH / Carragher B / Potter CS
CitationJournal: J Struct Biol / Year: 2011
Title: Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy.
Authors: Anna-Clare Milazzo / Anchi Cheng / Arne Moeller / Dmitry Lyumkis / Erica Jacovetty / James Polukas / Mark H Ellisman / Nguyen-Huu Xuong / Bridget Carragher / Clinton S Potter /
Abstract: We report on initial results of using a new direct detection device (DDD) for single particle reconstruction of vitreous ice embedded specimens. Images were acquired on a Tecnai F20 at 200keV and a ...We report on initial results of using a new direct detection device (DDD) for single particle reconstruction of vitreous ice embedded specimens. Images were acquired on a Tecnai F20 at 200keV and a nominal magnification of 29,000×. This camera has a significantly improved signal to noise ratio and modulation transfer function (MTF) at 200keV compared to a standard CCD camera installed on the same microscope. Control of the DDD has been integrated into Leginon, an automated data collection system. Using GroEL as a test specimen, we obtained images of ∼30K particles with the CCD and the DDD from the same specimen sample using essentially identical imaging conditions. Comparison of the maps reconstructed from the CCD images and the DDD images demonstrates the improved performance of the DDD. We also obtained a 3D reconstruction from ∼70K GroEL particles acquired using the DDD; the quality of the density map demonstrates the potential of this new recording device for cryoEM data acquisition.
History
DepositionAug 30, 2011-
Header (metadata) releaseNov 28, 2011-
Map releaseNov 29, 2011-
UpdateNov 29, 2011-
Current statusNov 29, 2011Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5340_1.png

Downloads & links

-
Map

FileDownload / File: emd_5340.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAmplitude corrected and filtered GroEL map
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 1.8 / Movie #1: 1.8
Minimum - Maximum-6.87185 - 7.83067
Average (Standard dev.)-0.000000000215158 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 264.96 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z264.960264.960264.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-6.8727.831-0.000

-
Supplemental data

-
Sample components

-
Entire : GroEL

EntireName: GroEL
Components
  • Sample: GroEL
  • Protein or peptide: GroEL

-
Supramolecule #1000: GroEL

SupramoleculeName: GroEL / type: sample / ID: 1000 / Oligomeric state: D7 14-mer / Number unique components: 1
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

-
Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: GroEL / Number of copies: 1 / Oligomeric state: homotetradecamer / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5 / Details: 100mM HEPES, 10mM Mg(OAc)2, 10mM KOAc, 2mM DTT
GridDetails: Protochips C-flat grid, holey carbon with 2um holes and 2um spacing 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: OTHER
Details: Vitrification instrument: Vitrobot. Grid plasma cleaned for 20 seconds with Fischione 1020 plasma cleaner using 75 percent argon, 25 percent oxygen mix.
Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 uL sample applied to grid. Blot for 3.5 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 108695 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Gatan side-entry 626 cryostage / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 102 K / Max: 102 K / Average: 102 K
Alignment procedureLegacy - Astigmatism: The objective lens astigmatism was corrected automatically using Leginon
Legacy - Electron beam tilt params: beam tilt was less than 0.1 mrad
DateFeb 24, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 879 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: CTF correction of each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP
Details: Amplitude corrected with an x-ray scattering curve to 8A and low pass filtered to 7.5A
Number images used: 30711
DetailsThe particles were selected using an automatic selection program.

+
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