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- EMDB-9202: T20S proteasome using with published picks (EMPIAR-10025 reprocessing) -

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Basic information

Entry
Database: EMDB / ID: 9202
TitleT20S proteasome using with published picks (EMPIAR-10025 reprocessing)
Map dataCryoSparc v0 sharpened map from published picks.
SampleT20S proteasome:
SourceThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / 2.99 Å resolution
AuthorsBepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B
Citation
Journal: 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
#1: Journal: Elife / Year: 2015
Title: 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy.
Authors: Melody G Campbell / David Veesler / Anchi Cheng / Clinton S Potter / Bridget Carragher
DateDeposition: Oct 12, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 24, 2018 / Last update: Oct 24, 2018

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9202.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
0.66 Å/pix.
= 263. Å
400 pix
0.66 Å/pix.
= 263. Å
400 pix
0.66 Å/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
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-1.1195682 - 1.8708209
Average (Standard dev.)0.00072817766 (0.08289225)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 263.0 Å
α=β=γ: 90.0 deg.

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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.1201.8710.001

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Supplemental data

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Mask #1

Fileemd_9202_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire T20S proteasome

EntireName: T20S proteasome / Number of components: 1

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Component #1: protein, T20S proteasome

ProteinName: T20S proteasome / Recombinant expression: No
SourceSpecies: Thermoplasma acidophilum (acidophilic)
Source (engineered)Expression System: Thermoplasma acidophilum (acidophilic)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.21 mg/ml / Buffer solution: 20 mM Tris, 150 mM NaCl / pH: 7.8
Support filmunspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE
Details: Blot for 2.5 seconds before plunging. Vitrification carried out at room temperature..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 53 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 900.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D7 (2*7 fold dihedral) / Number of projections: 49954
Details: CryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
3D reconstructionSoftware: cryoSPARC / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Cryosparc v0 homogeneous refinement. / Euler angles: Cryosparc v0

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