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- EMDB-0530: AcrAB-TolC from cellular tomogram - a complete data processing wo... -

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Basic information

Entry
Database: EMDB / ID: EMD-0530
TitleAcrAB-TolC from cellular tomogram - a complete data processing workflow for CryoET and subtomogram averaging
Map dataAveraged structure of AcrAB-TolC pump from E. coli cellular tomograms
Sample
  • Complex: AcrAB-TolC multidrug efflux pump
Biological speciesEscherichia coli BL21(DE3) (bacteria)
Methodelectron tomography / cryo EM / Resolution: 15.0 Å
AuthorsChen M / Bell JM / Shi X / Wang Z / 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) releaseMar 6, 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: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0530.png

Downloads & links

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Map

FileDownload / File: emd_0530.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged structure of AcrAB-TolC pump from E. coli cellular tomograms
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.37 Å/pix.
x 140 pix.
= 471.24 Å		3.37 Å/pix.
x 140 pix.
= 471.24 Å		3.37 Å/pix.
x 140 pix.
= 471.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.366 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.6
Minimum - Maximum-1.7491268 - 3.6039977
Average (Standard dev.)0.015334747 (±0.14911146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 471.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.3663.3663.366
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z471.240471.240471.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-1.7493.6040.015

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Supplemental data

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Sample components

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Entire : AcrAB-TolC multidrug efflux pump

EntireName: AcrAB-TolC multidrug efflux pump
Components
  • Complex: AcrAB-TolC multidrug efflux pump

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Supramolecule #1: AcrAB-TolC multidrug efflux pump

SupramoleculeName: AcrAB-TolC multidrug efflux pump / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 740 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R3.5/1 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III
DetailsE. coli cell overexpressing AcrAB-TolC
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.3) / Number images used: 1321
CTF correctionSoftware - Name: EMAN2 (ver. 2.3)
FSC plot (resolution estimation)

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