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- EMDB-9194: T20S proteasome using Topaz at threshold t-3 (EMPIAR-10025 reproc... -

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Basic information

Entry
Database: EMDB / ID: EMD-9194
TitleT20S proteasome using Topaz at threshold t-3 (EMPIAR-10025 reprocessing)
Map dataCryosparc v0 sharpened map for Topaz t-3 threshold
Sample
  • Complex: T20S proteasome
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsBepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR01-GM081871 United States
Other privateSimons Foundation / SF349247 United States
National Institutes of Health/National Institute of General Medical SciencesF32GM128303 United States
National Institutes of Health/National Institute of General Medical SciencesGM103310 United States
Other governmentNYSTAR United States
National Institutes of Health/Office of the DirectorOD019994 United States
Other privateAgouron Institute / F00316 United States
CitationJournal: Res Comput Mol Biol / Year: 2018
Title: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.
Authors: Tristan Bepler / Andrew Morin / Alex J Noble / Julia Brasch / Lawrence Shapiro / Bonnie Berger /
History
DepositionOct 10, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 24, 2018-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9194.png

Downloads & links

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Map

FileDownload / File: emd_9194.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc v0 sharpened map for Topaz t-3 threshold
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 263. Å		0.66 Å/pix.
x 400 pix.
= 263. Å		0.66 Å/pix.
x 400 pix.
= 263. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6575 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.0757214 - 1.7427452
Average (Standard dev.)0.000746185 (±0.073432066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 263.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.65750.65750.6575
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z263.000263.000263.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.0761.7430.001

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Supplemental data

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Mask #1

Fileemd_9194_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc v0 unsharpened map for Topaz t-3 threshold

Fileemd_9194_additional.map
AnnotationCryosparc v0 unsharpened map for Topaz t-3 threshold
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc v0 unsharpened map for Topaz t-3 threshold

Fileemd_9194_additional_1.map
AnnotationCryosparc v0 unsharpened map for Topaz t-3 threshold
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryosparc v0 halfmap A for Topaz t-3 threshold

Fileemd_9194_half_map_1.map
AnnotationCryosparc v0 halfmap A for Topaz t-3 threshold
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryosparc v0 halfmap B for Topaz t-3 threshold

Fileemd_9194_half_map_2.map
AnnotationCryosparc v0 halfmap B for Topaz t-3 threshold
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T20S proteasome

EntireName: T20S proteasome
Components
  • Complex: T20S proteasome

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Supramolecule #1: T20S proteasome

SupramoleculeName: T20S proteasome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Recombinant expressionOrganism: Thermoplasma acidophilum (acidophilic)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.21 mg/mL
BufferpH: 7.8 / Details: 20 mM Tris, 150 mM NaCl
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3
Details: Blot for 2.5 seconds before plunging. Vitrification carried out at room temperature..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsCryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
Particle selectionNumber selected: 160658
Details: All initial particles were used in the final reconstruction; ie. no particle filtering or classification was performed.
Startup modelType of model: INSILICO MODEL / In silico model: Cryosparc v0 ab initio
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - Version: 0 / Details: CryoSparc v0 homogeneous 3D refinement. / Number images used: 160658
Initial angle assignmentType: OTHER / Details: Cryosparc v0
Final angle assignmentType: OTHER / Details: Cryosparc v0

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