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Open data
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Basic information
Entry | Database: PDB / ID: 8r7l | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the human TREX complex | ||||||||||||||||||||||||
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![]() | GENE REGULATION / mRNA export | ||||||||||||||||||||||||
Function / homology | ![]() THO complex / THO complex part of transcription export complex / transcription export complex / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript ...THO complex / THO complex part of transcription export complex / transcription export complex / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / ATP-dependent activity, acting on RNA / ATP-dependent protein binding / 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 / stem cell division / generation of neurons / spliceosomal complex assembly / blastocyst development / U6 snRNA binding / neuron development / mRNA export from nucleus / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / osteoblast differentiation / regulation of gene expression / negative regulation of neuron projection development / RNA helicase activity / nuclear speck / RNA helicase / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.12 Å | ||||||||||||||||||||||||
![]() | Hohmann, U. / Pacheco-Fiallos, B. / Plaschka, C. | ||||||||||||||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: A molecular switch orchestrates the export of human messenger RNA Authors: Hohmann, U. / Pacheco-Fiallos, B. / Brennecke, J. / Plaschka, C. | ||||||||||||||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 369.8 KB | Display | ![]() |
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PDB format | ![]() | 279.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 65.2 KB | Display | |
Data in CIF | ![]() | 99.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18979MC ![]() 8r7jC ![]() 8r7kC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 49056.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 75752.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 183087.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 38817.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 19233.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human TREX complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 750 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204147 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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