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- EMDB-8589: Subtomogram average of microtubules from Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-8589
TitleSubtomogram average of microtubules from Trypanosoma brucei
Map dataSubtomogram average of microtubules from Trypanosoma brucei
Sample
  • Complex: Microtubule
Biological speciesTrypanosoma brucei (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 55.0 Å
AuthorsChen M / Sun SY / Ludtke SJ / He CY / Schmid MF / Chiu W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139,P01NS092525, P41GM103832 United States
CitationJournal: Nat Methods / Year: 2017
Title: Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Authors: Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke /
Abstract: Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components ...Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package.
History
DepositionFeb 3, 2017-
Header (metadata) releaseMar 1, 2017-
Map releaseMar 1, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8589.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of microtubules from Trypanosoma brucei
Voxel size
XYZ
EMDB info.5.35.35.3
CCP4 map header222
EM Navigator Movie #1222
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.12275627 - 0.17894378
Average (Standard dev.)0.00026404572 (±0.019319996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin22955185970190968033
Dimensions192192192
Spacing192192192
CellA=B=C: 1017.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1600.3340.002

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Supplemental data

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Sample components

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Entire : Microtubule

EntireName: Microtubule
Components
  • Complex: Microtubule

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Supramolecule #1: Microtubule

SupramoleculeName: Microtubule / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Trypanosoma brucei (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: INTEGRATING / Average electron dose: 2.0 e/Å2

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Image processing

ExtractionNumber tomograms: 1 / Number images used: 511 / Reference model: Reference free averaging / Method: Automated tomogram segmentation / Software - Name: EMAN (ver. 2.2) / Software - details: Tomoseg tool
Final angle assignmentType: OTHER / Software - Name: EMAN (ver. 2.2) / Details: Single particle tomography tool in EMAN2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 55.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number subtomograms used: 511

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