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- EMDB-14806: Structure of an endogenous human TREX complex bound to mRNA, map B -

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Basic information

Entry
Database: EMDB / ID: EMD-14806
TitleStructure of an endogenous human TREX complex bound to mRNA, map B
Map dataendogenous TREX-mRNA, focused map B, unsharpened map
Sample
  • Complex: endogenous human TREX-mRNA complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
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
DepositionApr 21, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14806.png

Downloads & links

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Map

FileDownload / File: emd_14806.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationendogenous TREX-mRNA, focused map B, unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 416 pix.
= 586.56 Å		1.41 Å/pix.
x 416 pix.
= 586.56 Å		1.41 Å/pix.
x 416 pix.
= 586.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.8615109 - 2.3579276
Average (Standard dev.)0.011186772 (±0.07931836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 586.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14806_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: endogenous TREX-mRNA, focused map B, sharpened map

Fileemd_14806_additional_1.map
Annotationendogenous TREX-mRNA, focused map B, sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: endogenous TREX-mRNA, focused map B, half map

Fileemd_14806_half_map_1.map
Annotationendogenous TREX-mRNA, focused map B, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: endogenous TREX-mRNA, focused map B, half map

Fileemd_14806_half_map_2.map
Annotationendogenous TREX-mRNA, focused map B, half 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 : endogenous human TREX-mRNA complex

EntireName: endogenous human TREX-mRNA complex
Components
  • Complex: endogenous human TREX-mRNA complex

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Supramolecule #1: endogenous human TREX-mRNA complex

SupramoleculeName: endogenous human TREX-mRNA complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.8 MDa

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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

Concentration0.2 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

11857

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61269
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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