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Yorodumi- EMDB-14804: Structure of an endogenous human TREX complex bound to mRNA, comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14804 | |||||||||
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Title | Structure of an endogenous human TREX complex bound to mRNA, composite map | |||||||||
Map data | TREX-mRNA composite map generated from sharpened focused maps A (EMD 14805),B (EMD-14806) and C (EMD-14807 ) | |||||||||
Sample |
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Keywords | transcription and export complex / TREX / RNA export / RNA packaging / RNA binding protein / gene expression / GENE REGULATION | |||||||||
Function / homology | Function and homology information THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / Transport of the SLBP independent Mature mRNA ...THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ATP-dependent protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / U4 snRNP / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / monocyte differentiation / blastocyst development / neuron development / RHOBTB2 GTPase cycle / mRNA export from nucleus / U6 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / osteoblast differentiation / Signaling by CSF1 (M-CSF) in myeloid cells / negative regulation of neuron projection development / regulation of gene expression / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_14804.map.gz | 8.2 MB | EMDB map data format | |
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Header (meta data) | emd-14804-v30.xml emd-14804.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
Images | emd_14804.png | 118.2 KB | ||
Filedesc metadata | emd-14804.cif.gz | 8.5 KB | ||
Others | emd_14804_additional_1.map.gz | 8.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14804 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14804 | HTTPS FTP |
-Validation report
Summary document | emd_14804_validation.pdf.gz | 360.6 KB | Display | EMDB validaton report |
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Full document | emd_14804_full_validation.pdf.gz | 360.1 KB | Display | |
Data in XML | emd_14804_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_14804_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14804 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14804 | HTTPS FTP |
-Related structure data
Related structure data | 7znkMC 7znjC 7znlC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14804.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | TREX-mRNA composite map generated from sharpened focused maps A (EMD 14805),B (EMD-14806) and C (EMD-14807 ) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.41 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: TREX-mRNA composite map generated from unsharpened focused maps...
File | emd_14804_additional_1.map | ||||||||||||
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Annotation | TREX-mRNA composite map generated from unsharpened focused maps A (EMD 14805),B (EMD-14806) and C (EMD-14807 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : endogenous human TREX-mRNA complex
+Supramolecule #1: endogenous human TREX-mRNA complex
+Macromolecule #1: RNA
+Macromolecule #2: THO complex subunit 1
+Macromolecule #3: THO complex subunit 2
+Macromolecule #4: THO complex subunit 3
+Macromolecule #5: THO complex subunit 5 homolog
+Macromolecule #6: THO complex subunit 6 homolog
+Macromolecule #7: THO complex subunit 7 homolog
+Macromolecule #8: Spliceosome RNA helicase DDX39B
+Macromolecule #9: THO complex subunit 4
-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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182534 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |