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- EMDB-16633: Structure of an ALYREF-exon junction complex hexamer, obtained fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-16633
TitleStructure of an ALYREF-exon junction complex hexamer, obtained from TREX-EJC-RNA sample
Map dataALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, sharpened
Sample
  • Complex: Hexameric complex between the TREX subunit ALYREF and the exon junction complex, obtained from TREX-EJC-RNA sample
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPacheco-Fiallos FB / Vorlaender MK / Plaschka C
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)European 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 3, 2023-
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_16633.png

Downloads & links

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Map

FileDownload / File: emd_16633.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, sharpened
Voxel sizeX=Y=Z: 1.325 Å
Density
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-6.413904 - 9.532971
Average (Standard dev.)0.03097729 (±0.24483201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16633_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, unsharpened

Fileemd_16633_additional_1.map
AnnotationALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map

Fileemd_16633_half_map_1.map
AnnotationALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map

Fileemd_16633_half_map_2.map
AnnotationALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, 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 : Hexameric complex between the TREX subunit ALYREF and the exon ju...

EntireName: Hexameric complex between the TREX subunit ALYREF and the exon junction complex, obtained from TREX-EJC-RNA sample
Components
  • Complex: Hexameric complex between the TREX subunit ALYREF and the exon junction complex, obtained from TREX-EJC-RNA sample

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Supramolecule #1: Hexameric complex between the TREX subunit ALYREF and the exon ju...

SupramoleculeName: Hexameric complex between the TREX subunit ALYREF and the exon junction complex, obtained from TREX-EJC-RNA sample
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 650 KDa

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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: 63.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - Version: 0
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 383510
FSC plot (resolution estimation)

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