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- EMDB-6219: T. acidophilum 20S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-6219
TitleT. acidophilum 20S proteasome
Map dataReconstruction of T. acidophilum 20S proteasome, using K2 summit camera at a low magnification
Sample
  • Sample: T. acidophilum 20S proteasome
  • Protein or peptide: 20S proteasome
KeywordsT. acidophilum 20S proteasome
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLi X / Cheng Y
CitationJournal: Nat Methods / Year: 2015
Title: De novo protein structure determination from near-atomic-resolution cryo-EM maps.
Authors: Ray Yu-Ruei Wang / Mikhail Kudryashev / Xueming Li / Edward H Egelman / Marek Basler / Yifan Cheng / David Baker / Frank DiMaio /
Abstract: We present a de novo model-building approach that combines predicted backbone conformations with side-chain fit to density to accurately assign sequence into density maps. This method yielded ...We present a de novo model-building approach that combines predicted backbone conformations with side-chain fit to density to accurately assign sequence into density maps. This method yielded accurate models for six of nine experimental maps at 3.3- to 4.8-Å resolution and produced a nearly complete model for an unsolved map containing a 660-residue heterodimeric protein. This method should enable rapid and reliable protein structure determination from near-atomic-resolution cryo-electron microscopy (cryo-EM) maps.
History
DepositionDec 19, 2014-
Header (metadata) releaseJan 21, 2015-
Map releaseJan 21, 2015-
UpdateJan 21, 2015-
Current statusJan 21, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6219.gif

Downloads & links

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Map

FileDownload / File: emd_6219.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of T. acidophilum 20S proteasome, using K2 summit camera at a low magnification
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 320 pix.
= 313.6 Å		0.98 Å/pix.
x 320 pix.
= 313.6 Å		0.98 Å/pix.
x 320 pix.
= 313.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-7.99466181 - 16.68803024
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 313.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z313.600313.600313.600
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/NS320320320
D min/max/mean-7.99516.688-0.000

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Supplemental data

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Sample components

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Entire : T. acidophilum 20S proteasome

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

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Supramolecule #1000: T. acidophilum 20S proteasome

SupramoleculeName: T. acidophilum 20S proteasome / type: sample / ID: 1000 / Oligomeric state: 28-mer / Number unique components: 1
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa

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Macromolecule #1: 20S proteasome

MacromoleculeName: 20S proteasome / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 24-mer / Recombinant expression: Yes
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightExperimental: 700 KDa / Theoretical: 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

GridDetails: Holey carbon on top of 400 mesh grid
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
DetailsImages were recorded in dose-fractionated format using K2 Summit operated in counting and super-resolution mode. Motion correction was performed for each image.
DateJan 1, 2012
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 157 / Average electron dose: 30 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: 1.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 20000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: OTHER / Software - Name: FREALIGN / Number images used: 79801

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