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- EMDB-4244: High-resolution cryo-EM structure of the human 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: 4244
TitleHigh-resolution cryo-EM structure of the human 80S ribosome
Map data
Sample80S ribosome with ligand HHT and HYG:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 2.9 Å resolution
AuthorsNatchiar SK / Myasnikov AG
CitationJournal: Nature / Year: 2017
Title: Visualization of chemical modifications in the human 80S ribosome structure.
Authors: S Kundhavai Natchiar / Alexander G Myasnikov / Hanna Kratzat / Isabelle Hazemann / Bruno P Klaholz
DateDeposition: Jan 2, 2018 / Header (metadata) release: Jan 24, 2018 / Map release: Jan 24, 2018 / Last update: Jan 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4244.map.gz (map file in CCP4 format, 1048577 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
640 pix
0.9 Å/pix.
= 576. Å
640 pix
0.9 Å/pix.
= 576. Å
640 pix
0.9 Å/pix.
= 576. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density
Contour Level:0.007 (by author), 0.02 (movie #1):
Minimum - Maximum-0.18992385 - 0.30064753
Average (Standard dev.)0.000021191163 (0.0031622127)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions640640640
Origin0.00.00.0
Limit639.0639.0639.0
Spacing640640640
CellA=B=C: 576.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.90.90.9
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z576.000576.000576.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS640640640
D min/max/mean-0.1900.3010.000

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Supplemental data

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Mask #1

Fileemd_4244_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire 80S ribosome with ligand HHT and HYG

EntireName: 80S ribosome with ligand HHT and HYG / Details: Human 80S ribosome with modified nucleotides / Number of components: 1

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Component #1: protein, 80S ribosome with ligand HHT and HYG

ProteinName: 80S ribosome with ligand HHT and HYG / Details: Human 80S ribosome with modified nucleotides / Recombinant expression: No
MassExperimental: 4.3 MDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml
Buffer solution: 100mM KCl, 5mM MgAc2, 20mM Hepes, 10mM NH4Cl
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.5 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 138234
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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