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- EMDB-61462: Cryo-EM structure of a protein-free RNA at 2.17 angstrom resoluti... -

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Basic information

Entry
Database: EMDB / ID: EMD-61462
TitleCryo-EM structure of a protein-free RNA at 2.17 angstrom resolution from Biortus
Map data
Sample
  • Organelle or cellular component: RNA from Tetrahymena ribozyme
KeywordsProtein-free RNA / RNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsWang M / Yang Y / Xu L / Shi H / Zhao L / Han T / Hu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of a protein-free RNA at 2.17 angstrom resolution from Biortus
Authors: Wang M / Yang Y / Xu L / Shi H / Zhao L / Han T / Hu Y
History
DepositionSep 6, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61462.png

Downloads & links

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Map

FileDownload / File: emd_61462.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 512 pix.
= 296.96 Å		0.58 Å/pix.
x 512 pix.
= 296.96 Å		0.58 Å/pix.
x 512 pix.
= 296.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.074
Minimum - Maximum-0.1767572 - 0.5634007
Average (Standard dev.)0.00008430176 (±0.007239248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 296.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61462_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61462_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61462_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 : RNA from Tetrahymena ribozyme

EntireName: RNA from Tetrahymena ribozyme
Components
  • Organelle or cellular component: RNA from Tetrahymena ribozyme

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Supramolecule #1: RNA from Tetrahymena ribozyme

SupramoleculeName: RNA from Tetrahymena ribozyme / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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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

BufferpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 422469
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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