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- EMDB-23357: Structure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-23357
TitleStructure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution
Map dataStructure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution
Sample
  • Complex: 80S ribsome from Oryctolagus cuniculus
Biological speciesOryctolagus cuniculus (rabbit)
Methodsubtomogram averaging / cryo EM / Resolution: 5.6 Å
AuthorsBouvette J / Liu HF / Du X / Zhou Y / Sikkema AP / Mello JFR / Klemm B / Huang R / Schaaper RM / Borgnia MJ / Bartesaghi A
CitationJournal: Nat Commun / Year: 2021
Title: Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.
Authors: Bouvette J / Liu HF / Du X / Zhou Y / Sikkema AP / da Fonseca Rezende E Mello J / Klemm BP / Huang R / Schaaper RM / Borgnia MJ / Bartesaghi A
History
DepositionJan 26, 2021-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23357.png

Downloads & links

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Map

FileDownload / File: emd_23357.map.gz / Format: CCP4 / Size: 5.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
2.62 Å/pix.
x 114 pix.
= 298.68 Å		2.62 Å/pix.
x 106 pix.
= 277.72 Å		2.62 Å/pix.
x 129 pix.
= 337.98 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.1837952 - 0.20162033
Average (Standard dev.)-2.9403872e-13 (±0.018231615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin825064
Dimensions106129114
Spacing114106129
CellA: 298.68 Å / B: 277.72 Å / C: 337.97998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z114106129
origin x/y/z0.0000.0000.000
length x/y/z298.680277.720337.980
α/β/γ90.00090.00090.000
start NX/NY/NZ648250
NX/NY/NZ114106129
MAP C/R/S321
start NC/NR/NS508264
NC/NR/NS129106114
D min/max/mean-0.1840.202-0.000

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Supplemental data

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Mask #1

Fileemd_23357_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Structure of 80S ribosome from EMPIAR-10064 at 5.6...

Fileemd_23357_additional_1.map
AnnotationStructure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of 80S ribosome from EMPIAR-10064 at 5.6...

Fileemd_23357_half_map_1.map
AnnotationStructure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of 80S ribosome from EMPIAR-10064 at 5.6...

Fileemd_23357_half_map_2.map
AnnotationStructure of 80S ribosome from EMPIAR-10064 at 5.6 Angstrom Resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S ribsome from Oryctolagus cuniculus

EntireName: 80S ribsome from Oryctolagus cuniculus
Components
  • Complex: 80S ribsome from Oryctolagus cuniculus

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Supramolecule #1: 80S ribsome from Oryctolagus cuniculus

SupramoleculeName: 80S ribsome from Oryctolagus cuniculus / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 4286
ExtractionNumber tomograms: 4 / Number images used: 4286 / Method: Manually picked
Final 3D classificationNumber classes: 1
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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