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Yorodumi- EMDB-16633: Structure of an ALYREF-exon junction complex hexamer, obtained fr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16633 | |||||||||
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Title | Structure of an ALYREF-exon junction complex hexamer, obtained from TREX-EJC-RNA sample | |||||||||
Map data | ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, sharpened | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Pacheco-Fiallos FB / Vorlaender MK / Plaschka C | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16633.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-16633-v30.xml emd-16633.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16633_fsc.xml | 8.8 KB | Display | FSC data file |
Images | emd_16633.png | 176.7 KB | ||
Masks | emd_16633_msk_1.map | 64 MB | Mask map | |
Others | emd_16633_additional_1.map.gz emd_16633_half_map_1.map.gz emd_16633_half_map_2.map.gz | 30.4 MB 58.5 MB 58.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16633 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16633 | HTTPS FTP |
-Validation report
Summary document | emd_16633_validation.pdf.gz | 806.4 KB | Display | EMDB validaton report |
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Full document | emd_16633_full_validation.pdf.gz | 806 KB | Display | |
Data in XML | emd_16633_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_16633_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16633 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16633 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16633.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, sharpened | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.325 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16633_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, unsharpened
File | emd_16633_additional_1.map | ||||||||||||
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Annotation | ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map
File | emd_16633_half_map_1.map | ||||||||||||
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Annotation | ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map
File | emd_16633_half_map_2.map | ||||||||||||
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Annotation | ALYREF-EJC-RNA map, obtained from TREX-EJC-RNA sample, half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hexameric complex between the TREX subunit ALYREF and the exon ju...
Entire | Name: Hexameric complex between the TREX subunit ALYREF and the exon junction complex, obtained from TREX-EJC-RNA sample |
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Components |
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-Supramolecule #1: Hexameric complex between the TREX subunit ALYREF and the exon ju...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 650 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.9 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |