+Open data
-Basic information
Entry | Database: PDB / ID: 7znj | |||||||||
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Title | Structure of an ALYREF-exon junction complex hexamer | |||||||||
Components |
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Keywords | GENE REGULATION / transcription-exort complex / TREX / splicing / exon junction complex / EJC / RNA export / RNA binding proteins | |||||||||
Function / homology | Function and homology information exon-exon junction subcomplex mago-y14 / transcription export complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / C5-methylcytidine-containing RNA reader activity / cellular response to selenite ion / exon-exon junction complex / selenocysteine insertion sequence binding / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential ...exon-exon junction subcomplex mago-y14 / transcription export complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / C5-methylcytidine-containing RNA reader activity / cellular response to selenite ion / exon-exon junction complex / selenocysteine insertion sequence binding / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of mRNA processing / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / embryonic cranial skeleton morphogenesis / U2-type catalytic step 1 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / exploration behavior / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of alternative mRNA splicing, via spliceosome / associative learning / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to brain-derived neurotrophic factor stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of translation / response to organic cyclic compound / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / RNA stem-loop binding / rRNA processing / regulation of translation / outer membrane-bounded periplasmic space / postsynapse / RNA helicase activity / negative regulation of translation / RNA helicase / nuclear speck / mRNA binding / neuronal cell body / glutamatergic synapse / dendrite / nucleolus / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Pacheco-Fiallos, F.B. / Vorlaender, M.K. / Plaschka, C. | |||||||||
Funding support | European Union, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7znj.cif.gz | 899.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7znj.ent.gz | 700.7 KB | Display | PDB format |
PDBx/mmJSON format | 7znj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7znj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7znj_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7znj_validation.xml.gz | 113 KB | Display | |
Data in CIF | 7znj_validation.cif.gz | 174.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/7znj ftp://data.pdbj.org/pub/pdb/validation_reports/zn/7znj | HTTPS FTP |
-Related structure data
Related structure data | 14803MC 7znkC 7znlC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 24 molecules AaFfKkBbGgLlCcHhMmDdIiNn
#1: Protein | Mass: 43819.367 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A3, DDX48, KIAA0111 / Production host: Escherichia coli (E. coli) / References: UniProt: P38919 #2: Protein | Mass: 17189.625 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAGOH, MAGOHA / Production host: Escherichia coli (E. coli) / References: UniProt: P61326 #3: Protein | Mass: 10370.525 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM8A, RBM8, HSPC114, MDS014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5S9 #4: Protein | Mass: 57598.855 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: malE, Z5632, ECs5017, ALYREF, ALY, BEF, THOC4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY0, UniProt: Q86V81 |
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-RNA chain , 1 types, 6 molecules EeJjOo
#5: RNA chain | Mass: 1792.037 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 2 types, 12 molecules
#6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ANP / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hexameric complex between the TREX subunit ALYREF and the exon junction complex Type: COMPLEX Details: Assembled with truncated MBP-tagged ALYREF (residues 55-183) Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 0.65 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1564602 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.44 Å2 | ||||||||||||||||||||||||
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