+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16753 | |||||||||
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Title | Tomogram of purified human TREX-mRNPs | |||||||||
Map data | Reconstructed tomogram (denoised) | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
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_16753.map.gz | 368.5 MB | EMDB map data format | |
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Header (meta data) | emd-16753-v30.xml emd-16753.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
Images | emd_16753.png | 167.1 KB | ||
Others | emd_16753_additional_1.map.gz emd_16753_additional_2.map.gz emd_16753_additional_3.map.gz emd_16753_additional_4.map.gz | 20.5 MB 20.5 MB 20.6 MB 368.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16753 | HTTPS FTP |
-Validation report
Summary document | emd_16753_validation.pdf.gz | 418.2 KB | Display | EMDB validaton report |
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Full document | emd_16753_full_validation.pdf.gz | 417.7 KB | Display | |
Data in XML | emd_16753_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | emd_16753_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16753 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16753 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16753.map.gz / Format: CCP4 / Size: 397.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | Reconstructed tomogram (denoised) | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sub-tomogram average map of TREX bound to mRNPs,...
File | emd_16753_additional_1.map | ||||||||||||
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Annotation | Sub-tomogram average map of TREX bound to mRNPs, post-processed with wide mask | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sub-tomogram average map of TREX bound to mRNPs,...
File | emd_16753_additional_2.map | ||||||||||||
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Annotation | Sub-tomogram average map of TREX bound to mRNPs, post-processed with mask on THOC-5, -6, -7 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sub-tomogram average map of TREX bound to mRNPs,...
File | emd_16753_additional_3.map | ||||||||||||
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Annotation | Sub-tomogram average map of TREX bound to mRNPs, post-processed with mask on THOC-1, -2, -3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed tomogram
File | emd_16753_additional_4.map | ||||||||||||
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Annotation | Reconstructed tomogram | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : endogenous human transcription-export complex
Entire | Name: endogenous human transcription-export complex |
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Components |
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-Supramolecule #1: endogenous human transcription-export complex
Supramolecule | Name: endogenous human transcription-export complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: K562 cells |
Molecular weight | Theoretical: 1.8 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 295 K |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: Warp / Number images used: 61 |
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