[English] 日本語
Yorodumi
- EMDB-2838: Cryo-EM structure of TMV reconstructed from data ranging from 14.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2838
TitleCryo-EM structure of TMV reconstructed from data ranging from 14.3-18.4 e-/A^2 accumulated dose
Map dataCryo-EM structure of TMV reconstructed from data ranging from 14.3-18.4 e-/A^2 accumulated dose
Sample
  • Sample: Tobacco Mosaic Virus
  • Virus: Tobacco mosaic virus
Keywordstobacco mosaic virus / direct electron detectors / single particle helical reconstruction / radiation damage
Biological speciesTobacco mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFromm SA / Bharat TAM / Jakobi AJ / Hagen WJH / Sachse C
CitationJournal: J Struct Biol / Year: 2015
Title: Seeing tobacco mosaic virus through direct electron detectors.
Authors: Simon A Fromm / Tanmay A M Bharat / Arjen J Jakobi / Wim J H Hagen / Carsten Sachse /
Abstract: With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require ...With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2Å in resolution using cryo-EM.
History
DepositionDec 10, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseDec 24, 2014-
UpdateMar 11, 2015-
Current statusMar 11, 2015Processing 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 cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2838.png

Downloads & links

-
Map

FileDownload / File: emd_2838.map.gz / Format: CCP4 / Size: 31.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of TMV reconstructed from data ranging from 14.3-18.4 e-/A^2 accumulated dose
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 190 pix.
= 201.78 Å		1.06 Å/pix.
x 210 pix.
= 223.02 Å		1.06 Å/pix.
x 210 pix.
= 223.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-3.44806886 - 5.45982599
Average (Standard dev.)0.01837258 (±0.74542463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-105-105-95
Dimensions210210190
Spacing210210190
CellA: 223.02 Å / B: 223.02 Å / C: 201.78001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z210210190
origin x/y/z0.0000.0000.000
length x/y/z223.020223.020201.780
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-105-105-95
NC/NR/NS210210190
D min/max/mean-3.4485.4600.018

-
Supplemental data

-
Sample components

-
Entire : Tobacco Mosaic Virus

EntireName: Tobacco Mosaic Virus
Components
  • Sample: Tobacco Mosaic Virus
  • Virus: Tobacco mosaic virus

-
Supramolecule #1000: Tobacco Mosaic Virus

SupramoleculeName: Tobacco Mosaic Virus / type: sample / ID: 1000 / Details: The sample was purified from infected leaves. / Oligomeric state: helical / Number unique components: 1
Molecular weightTheoretical: 39.5 MDa

-
Supramolecule #1: Tobacco mosaic virus

SupramoleculeName: Tobacco mosaic virus / type: virus / ID: 1 / Name.synonym: TMV / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Sci species strain: vulgare / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: TMV
Host (natural)Organism: Nicotiana tabacum (common tobacco) / synonym: PLANTAE(HIGHER PLANTS)
Molecular weightTheoretical: 39.5 MDa
Virus shellShell ID: 1 / Name: CP / Diameter: 180 Å

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration11.0 mg/mL
BufferpH: 7 / Details: 50 mM NaPO4
GridDetails: Quantifoil 2/2 Cu 200 mesh grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK III
Method: Blot for 8 seconds with an offset of -2 mm ~30-45 seconds after sample application

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: CTFTILT
DetailsNanoprobe mode, dose rate ~41 e-/px/s on the camera level, fully automated acquisition using FEI EPU software
DateOct 16, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 109 / Average electron dose: 30.7 e/Å2
Details: each micrograph was recorded as a movie of 7 frames excluding the roll-in frame corresponding to 2 e-/A^2 accumulated dose which was discarded
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 131827 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsImage processing was done using SPRING.
Final reconstructionApplied symmetry - Helical parameters - Δz: 1.408 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.03 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: SPRING
Details: final map was calculated only from frame 4 of each micrograph corresponding to an accumulated dose range of 14.3-18.4 e-/A^2
CTF correctionDetails: CTFTILT (specific for each segment)
Final angle assignmentDetails: SPIDER
FSC plot (resolution estimation)

+
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