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- EMDB-12531: T20S proteasome subtomogram average -

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Basic information

Entry
Database: EMDB / ID: EMD-12531
TitleT20S proteasome subtomogram average
Map dataT20S proteasome subtomogram average
Sample
  • Complex: T20S proteasome
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsubtomogram averaging / cryo EM / Resolution: 9.0 Å
AuthorsFernandez JJ
CitationJournal: J Struct Biol / Year: 2018
Title: Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion.
Authors: Jose-Jesus Fernandez / Sam Li / Tanmay A M Bharat / David A Agard /
Abstract: Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal ...Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET.
History
DepositionMar 3, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 10, 2021-
Current statusMar 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12531.png

Downloads & links

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Map

FileDownload / File: emd_12531.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT20S proteasome subtomogram average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.56 Å/pix.
x 120 pix.
= 307.2 Å		2.56 Å/pix.
x 120 pix.
= 307.2 Å		2.56 Å/pix.
x 120 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1e-07 / Movie #1: 0.1
Minimum - Maximum-0.4483154 - 0.42455736
Average (Standard dev.)0.0008088981 (±0.046153642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 307.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.562.562.56
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z307.200307.200307.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-170-170-170
NX/NY/NZ340340340
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.4480.4250.001

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Supplemental data

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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 / Macromolecule list: #1
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 3928
ExtractionNumber tomograms: 14 / Number images used: 3928
Final angle assignmentType: MAXIMUM LIKELIHOOD

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