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- EMDB-30868: liver ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-30868
Titleliver ribosome
Map data
Sample
  • Complex: liver ribosome
Biological speciesRibosome display vector pRDV (others)
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 Å
AuthorsZhang JG / Zhang DY / Sun L / Ji G / Huang XJ / Niu TX / Xu JS / Ma CY / Zhu Y / Gao N ...Zhang JG / Zhang DY / Sun L / Ji G / Huang XJ / Niu TX / Xu JS / Ma CY / Zhu Y / Gao N / Xu W / Sun F
CitationJournal: J.Struct.Biol. / Year: 2021
Title: VHUT-cryo-FIB, a method to fabricate frozen hydrated lamellae from tissue specimens for in situ cryo-electron tomography
Authors: Zhang J / Zhang D / Sun L / Ji G / Huang X / Niu T / Xu J / Ma C / Zhu Y / Gao N / Xu W / Sun F
History
DepositionJan 11, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateAug 3, 2022-
Current statusAug 3, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30868.png

Downloads & links

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Map

FileDownload / File: emd_30868.map.gz / Format: CCP4 / Size: 41.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 222 pix.
= 599.4 Å		2.7 Å/pix.
x 222 pix.
= 599.4 Å		2.7 Å/pix.
x 222 pix.
= 599.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.05 / Movie #1: 2.05
Minimum - Maximum-3.4019058 - 13.892037
Average (Standard dev.)0.10888205 (±0.7738001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions222222222
Spacing222222222
CellA=B=C: 599.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z222222222
origin x/y/z0.0000.0000.000
length x/y/z599.400599.400599.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS222222222
D min/max/mean-3.40213.8920.109

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Supplemental data

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Sample components

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Entire : liver ribosome

EntireName: liver ribosome
Components
  • Complex: liver ribosome

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Supramolecule #1: liver ribosome

SupramoleculeName: liver ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Ribosome display vector pRDV (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 13
ExtractionNumber tomograms: 13 / Number images used: 13
Final angle assignmentType: MAXIMUM LIKELIHOOD

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