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- EMDB-6245: Thermoplasma acidophilum 20S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-6245
TitleThermoplasma acidophilum 20S proteasome
Map dataThermoplasma acidophilum 20S proteasome. Reconstruction determined from the first 5,000 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: 4.1 Å
AuthorsLi X / Cheng Y
CitationJournal: Nat Methods / Year: 2015
Title: Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.
Authors: Frank DiMaio / Yifan Song / Xueming Li / Matthias J Brunner / Chunfu Xu / Vincent Conticello / Edward Egelman / Thomas Marlovits / Yifan Cheng / David Baker /
Abstract: We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local ...We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.
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_6245.gif

Downloads & links

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Map

FileDownload / File: emd_6245.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 5,000 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-6.92182255 - 17.906957630000001
Average (Standard dev.)0.0 (±1.0)
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-6.92217.907-0.000

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Supplemental data

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Supplemental map: emd 6245 half map 1.map

Fileemd_6245_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6245 half map 2.map

Fileemd_6245_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

GridDetails: Quantifoil
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: 4.1 Å / Resolution method: OTHER / Number images used: 5000

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