+Open data
-Basic information
Entry | Database: PDB / ID: 7apk | ||||||
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Title | Structure of the human THO - UAP56 complex | ||||||
Components |
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Keywords | GENE REGULATION / mRNA / nucleocytoplasmic transport / R-loop / gene expression | ||||||
Function / homology | Function and homology information THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent protein binding / mRNA 3'-end processing ...THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / mRNA Splicing - Major Pathway / RNA splicing / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / 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 / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Hohmann, U. / Puehringer, T. / Plaschka, C. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Elife / Year: 2020 Title: Structure of the human core transcription-export complex reveals a hub for multivalent interactions. Authors: Thomas Pühringer / Ulrich Hohmann / Laura Fin / Belén Pacheco-Fiallos / Ulla Schellhaas / Julius Brennecke / Clemens Plaschka / Abstract: The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and ...The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1-NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here, we report the cryo-electron microscopy structure of the human THO-UAP56/DDX39B complex at 3.3 Å resolution. The seven-subunit THO-UAP56/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX-mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7apk.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7apk.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7apk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7apk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7apk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7apk_validation.xml.gz | 195.6 KB | Display | |
Data in CIF | 7apk_validation.cif.gz | 333.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/7apk ftp://data.pdbj.org/pub/pdb/validation_reports/ap/7apk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-THO complex subunit ... , 6 types, 24 molecules AIaiBJbjCKckEMemFNfnGOgo
#1: Protein | Mass: 81138.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THOC1, HPR1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q96FV9 #2: Protein | Mass: 141584.594 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THOC2, CXorf3 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q8NI27 #3: Protein | Mass: 43279.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THOC3 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q96J01 #4: Protein | Mass: 78652.898 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THOC5, C22orf19, KIAA0983 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q13769 #5: Protein | Mass: 37577.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THOC6, WDR58, PSEC0006 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q86W42 #6: Protein | Mass: 23782.014 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THOC7, NIF3L1BP1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6I9Y2 |
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-Protein / Protein/peptide , 2 types, 6 molecules HPhpXx
#7: Protein | Mass: 51612.164 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39B, BAT1, UAP56 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q13838, RNA helicase #8: Protein/peptide | Mass: 3166.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 |
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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
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Molecular weight | Value: 1.836 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.9 | |||||||||||||||||||||||||
Buffer component |
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Specimen | 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: OTHER |
Electron lens | Mode: OTHER |
Image recording | Average exposure time: 3.8 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 26303 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||
Particle selection | Num. of particles selected: 1570265 | ||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195098 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |