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- EMDB-6244: Thermoplasma acidophilum 20S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-6244
TitleThermoplasma acidophilum 20S proteasome
Map dataThermoplasma acidophilum 20S proteasome. Reconstruction determined from the first 10,000 particles of a dataset used to calculate map EMD-5623.
Sample
  • Sample: Thermoplasma acidophilum 20S proteasome
  • Protein or peptide: Thermoplasma acidophilum 20S proteasome
KeywordsT. acidophilum 20S proteasome
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi X / Cheng Y
CitationJournal: J Struct Biol / Year: 2013
Title: Influence of electron dose rate on electron counting images recorded with the K2 camera.
Authors: Xueming Li / Shawn Q Zheng / Kiyoshi Egami / David A Agard / Yifan Cheng /
Abstract: A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor ...A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (~700 kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6 Å three-dimensional reconstruction from only 10,000 particles.
History
DepositionJan 19, 2015-
Header (metadata) releaseFeb 25, 2015-
Map releaseFeb 25, 2015-
UpdateFeb 25, 2015-
Current statusFeb 25, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6244.gif

Downloads & links

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Map

FileDownload / File: emd_6244.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThermoplasma acidophilum 20S proteasome. Reconstruction determined from the first 10,000 particles of a dataset used to calculate map EMD-5623.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 256 pix.
= 311.194 Å		1.22 Å/pix.
x 256 pix.
= 311.194 Å		1.22 Å/pix.
x 256 pix.
= 311.194 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-7.9654727 - 19.468698499999999
Average (Standard dev.)-0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 311.1936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21560156251.21560156251.2156015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z311.194311.194311.194
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-7.96519.469-0.000

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Supplemental data

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Supplemental map: emd 6244 half map 1.map

Fileemd_6244_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6244 half map 2.map

Fileemd_6244_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Thermoplasma acidophilum 20S proteasome

EntireName: Thermoplasma acidophilum 20S proteasome
Components
  • Sample: Thermoplasma acidophilum 20S proteasome
  • Protein or peptide: Thermoplasma acidophilum 20S proteasome

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Supramolecule #1000: Thermoplasma acidophilum 20S proteasome

SupramoleculeName: Thermoplasma acidophilum 20S proteasome / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: 28-mer / Number unique components: 1
Molecular weightExperimental: 700 KDa

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Macromolecule #1: Thermoplasma acidophilum 20S proteasome

MacromoleculeName: Thermoplasma acidophilum 20S proteasome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: 28-mer / Recombinant expression: Yes
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightExperimental: 700 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
DateJan 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsFREALIGN
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Number images used: 10000

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