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- EMDB-0529: Purified ribosome - A complete data processing workflow for CryoE... -

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Basic information

Entry
Database: EMDB / ID: EMD-0529
TitlePurified ribosome - A complete data processing workflow for CryoET and subtomogram averaging
Map dataAveraged structure of purified ribosome from EMPIAR-10064 dataset, after subtilt refinement in EMAN2.
Sample
  • Complex: Ribosome from EMPIAR-10064, MixedCTEM dataset
Biological speciesOryctolagus cuniculus (rabbit)
Methodelectron tomography / cryo EM / Resolution: 8.4 Å
AuthorsChen M / Bell JM / Ludtke SJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM080139 United States
CitationJournal: Nat Methods / Year: 2019
Title: A complete data processing workflow for cryo-ET and subtomogram averaging.
Authors: Muyuan Chen / James M Bell / Xiaodong Shi / Stella Y Sun / Zhao Wang / Steven J Ludtke /
Abstract: Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data ...Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, data processing is very labor intensive and the results are often limited by the skills of the personnel rather than the data. We present an integrated workflow that covers the entire tomography data processing pipeline, from automated tilt series alignment to subnanometer resolution subtomogram averaging. Resolution enhancement is made possible through the use of per-particle per-tilt contrast transfer function correction and alignment. The workflow greatly reduces human bias, increases throughput and more closely approaches data-limited resolution for subtomogram averaging in both purified macromolecules and cells.
History
DepositionFeb 7, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseOct 30, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0529.png

Downloads & links

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Map

FileDownload / File: emd_0529.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged structure of purified ribosome from EMPIAR-10064 dataset, after subtilt refinement in EMAN2.
Voxel sizeX=Y=Z: 2.62 Å
Density
Contour LevelMovie #1: 1
Minimum - Maximum-2.7292383 - 6.8252907
Average (Standard dev.)0.062119965 (±0.4563232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 471.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z471.600471.600471.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-2.7296.8250.062

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Supplemental data

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Additional map: Averaged structure after subtomogram refinement but before subtilt...

Fileemd_0529_additional.map
AnnotationAveraged structure after subtomogram refinement but before subtilt refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ribosome from EMPIAR-10064, MixedCTEM dataset

EntireName: Ribosome from EMPIAR-10064, MixedCTEM dataset
Components
  • Complex: Ribosome from EMPIAR-10064, MixedCTEM dataset

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Supramolecule #1: Ribosome from EMPIAR-10064, MixedCTEM dataset

SupramoleculeName: Ribosome from EMPIAR-10064, MixedCTEM dataset / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridDetails: unspecified
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: EMAN2 (ver. 2.3)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.3) / Number images used: 3239
FSC plot (resolution estimation)

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