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- EMDB-9201: T20S proteasome using Topaz at threshold t-3 with published picks... -

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Basic information

Entry
Database: EMDB / ID: EMD-9201
TitleT20S proteasome using Topaz at threshold t-3 with published picks subtracted from Topaz (EMPIAR-10025 reprocessing)
Map data
SampleT20S proteasome
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
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 /
Abstract: Recent developments in detector hardware and image-processing software have revolutionized single particle cryo-electron microscopy (cryoEM) and led to a wave of near-atomic resolution (typically ...Recent developments in detector hardware and image-processing software have revolutionized single particle cryo-electron microscopy (cryoEM) and led to a wave of near-atomic resolution (typically ∼3.3 Å) reconstructions. Reaching resolutions higher than 3 Å is a prerequisite for structure-based drug design and for cryoEM to become widely interesting to pharmaceutical industries. We report here the structure of the 700 kDa Thermoplasma acidophilum 20S proteasome (T20S), determined at 2.8 Å resolution by single-particle cryoEM. The quality of the reconstruction enables identifying the rotameric conformation adopted by some amino-acid side chains (rotamers) and resolving ordered water molecules, in agreement with the expectations for crystal structures at similar resolutions. The results described in this manuscript demonstrate that single particle cryoEM is capable of competing with X-ray crystallography for determination of protein structures of suitable quality for rational drug design.
History
DepositionOct 12, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 24, 2018-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing 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
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9201.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.9381096 - 1.6603535
Average (Standard dev.)0.00067304197 (±0.06960318)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.9381.6600.001

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Supplemental data

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Segmentation: #1

Fileemd_9201_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: Cryosparc v0 unsharpened map

Fileemd_9201_additional.map
AnnotationCryosparc v0 unsharpened map
Projections & Slices
AxesZYX

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Half map: Cryosparc v0 half-map

Fileemd_9201_half_map_1.map
AnnotationCryosparc v0 half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Cryosparc v0 half-map

Fileemd_9201_half_map_2.map
AnnotationCryosparc v0 half-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 (2x7 fold dihedral) / Number of projections: 109780
Details: CryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
3D reconstructionSoftware: cryoSPARC / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Cryosparc v0

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