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- EMDB-16951: cryo-EM structure of human tRNA(AspGUC) - PUS4 and PUS7 modified -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-16951
Titlecryo-EM structure of human tRNA(AspGUC) - PUS4 and PUS7 modified
Map datamain map
Sample
  • Complex: free Asp tRNA
KeywordstRNA / human / RNA
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.83 Å
AuthorsBiela AP
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: To Be Published
Title: Structures of human tRNAs by single particle cryo-EM
Authors: Biela AD / Biela AP / Lin TY / Glatt S
History
DepositionMar 30, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16951.png

Downloads & links

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Map

FileDownload / File: emd_16951.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 128 pix.
= 216.576 Å		1.69 Å/pix.
x 128 pix.
= 216.576 Å		1.69 Å/pix.
x 128 pix.
= 216.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.692 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.59
Minimum - Maximum-4.2268095 - 7.510343
Average (Standard dev.)0.006296379 (±0.1989369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 216.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_16951_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_16951_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : free Asp tRNA

EntireName: free Asp tRNA
Components
  • Complex: free Asp tRNA

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Supramolecule #1: free Asp tRNA

SupramoleculeName: free Asp tRNA / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Details: 8mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7511 / Average electron dose: 40.0 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 / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 676016
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 81488
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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