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- EMDB-16753: Tomogram of purified human TREX-mRNPs -

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Basic information

Entry
Database: EMDB / ID: EMD-16753
TitleTomogram of purified human TREX-mRNPs
Map dataReconstructed tomogram (denoised)
Sample
  • Complex: endogenous human transcription-export complex
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsPacheco-Fiallos FB / Vorlaender MK / Plaschka C
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
European Molecular Biology Organization (EMBO)623-2020European Union
CitationJournal: Nature / Year: 2023
Title: mRNA recognition and packaging by the human transcription-export complex.
Authors: Belén Pacheco-Fiallos / Matthias K Vorländer / Daria Riabov-Bassat / Laura Fin / Francis J O'Reilly / Farja I Ayala / Ulla Schellhaas / Juri Rappsilber / Clemens Plaschka /
Abstract: Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the ...Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
History
DepositionFeb 21, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16753.png

Downloads & links

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Map

FileDownload / File: emd_16753.map.gz / Format: CCP4 / Size: 397.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstructed tomogram (denoised)
Voxel sizeX=Y=Z: 10 Å
Density
Minimum - Maximum-0.20848206 - 0.52322316
Average (Standard dev.)-0.00067815324 (±0.01711818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions786566234
Spacing566786234
CellA: 5660.0 Å / B: 7860.0 Å / C: 2340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sub-tomogram average map of TREX bound to mRNPs,...

Fileemd_16753_additional_1.map
AnnotationSub-tomogram average map of TREX bound to mRNPs, post-processed with wide mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sub-tomogram average map of TREX bound to mRNPs,...

Fileemd_16753_additional_2.map
AnnotationSub-tomogram average map of TREX bound to mRNPs, post-processed with mask on THOC-5, -6, -7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sub-tomogram average map of TREX bound to mRNPs,...

Fileemd_16753_additional_3.map
AnnotationSub-tomogram average map of TREX bound to mRNPs, post-processed with mask on THOC-1, -2, -3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Reconstructed tomogram

Fileemd_16753_additional_4.map
AnnotationReconstructed tomogram
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : endogenous human transcription-export complex

EntireName: endogenous human transcription-export complex
Components
  • Complex: endogenous human transcription-export complex

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Supramolecule #1: endogenous human transcription-export complex

SupramoleculeName: endogenous human transcription-export complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: K562 cells
Molecular weightTheoretical: 1.8 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 295 K
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: Warp / Number images used: 61

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