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- EMDB-18510: PKR treated 48S late-stage initiation complex (phosphorylated eIF... -

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Basic information

Entry
Database: EMDB / ID: EMD-18510
TitlePKR treated 48S late-stage initiation complex (phosphorylated eIF2) with m6A mRNA
Map dataPKR-treated sample of m6A(-3) mRNA LS48SIC. Half map was resampled to 1.1A per pixel
Sample
  • Complex: 48S late-stage initiation complex with m6A-modified mRNA
Keywordstranslation initiation / ribosome / m6A / methylated mRNA / TRANSLATION
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGuca E / Lima LHF / Boissier F / Hashem Y
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: 48S late-stage initiation complex with m6A mRNA
Authors: Guca E / Lima LHF / Hashem Y
History
DepositionSep 25, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18510.png

Downloads & links

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Map

FileDownload / File: emd_18510.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPKR-treated sample of m6A(-3) mRNA LS48SIC. Half map was resampled to 1.1A per pixel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.07234495 - 0.1371159
Average (Standard dev.)-0.00000074909326 (±0.0046320856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: PKR-treated sample of m6A(-3) mRNA LS48SIC. Map was...

Fileemd_18510_half_map_1.map
AnnotationPKR-treated sample of m6A(-3) mRNA LS48SIC. Map was resampled to 1.1A per pixel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PKR-treated sample of m6A(-3) mRNA LS48SIC. Half map...

Fileemd_18510_half_map_2.map
AnnotationPKR-treated sample of m6A(-3) mRNA LS48SIC. Half map was resampled to 1.1A per pixel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 48S late-stage initiation complex with m6A-modified mRNA

EntireName: 48S late-stage initiation complex with m6A-modified mRNA
Components
  • Complex: 48S late-stage initiation complex with m6A-modified mRNA

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Supramolecule #1: 48S late-stage initiation complex with m6A-modified mRNA

SupramoleculeName: 48S late-stage initiation complex with m6A-modified mRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#40
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6yal

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78652
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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