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Open data
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Basic information
Entry | Database: PDB / ID: 5l3t | ||||||
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Title | Structure of the Saccharomyces cerevisiae TREX-2 complex | ||||||
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![]() | TRANSPORT PROTEIN / nuclear export / TREX-2 complex / Sac3 / Thp1 | ||||||
Function / homology | ![]() actin filament-based process / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / nuclear mRNA surveillance / nuclear pore cytoplasmic filaments / maintenance of DNA trinucleotide repeats / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / filamentous growth / mRNA 3'-end processing ...actin filament-based process / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / nuclear mRNA surveillance / nuclear pore cytoplasmic filaments / maintenance of DNA trinucleotide repeats / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / filamentous growth / mRNA 3'-end processing / proteasome regulatory particle, lid subcomplex / poly(A)+ mRNA export from nucleus / proteasome storage granule / proteasome assembly / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / protein folding chaperone / protein export from nucleus / proteasome complex / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / nuclear envelope / ribosomal small subunit biogenesis / mitotic cell cycle / ubiquitin-dependent protein catabolic process / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / regulation of cell cycle / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stewart, M. / Aibara, S. | ||||||
![]() | ![]() Title: The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region. Authors: Shintaro Aibara / Xiao-Chen Bai / Murray Stewart / ![]() Abstract: Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export- ...Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export-competent mRNPs through interactions with the general mRNA nuclear export factor Mex67:Mtr2. The TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31, and Sus1 bind. TREX-2 can be subdivided into two modules: one, in which Thp1 and Sem1 bind to the Sac3(M) region (residues ∼100-551), and the other in which Cdc31 and two Sus1 chains bind to the Sac3(CID) region (residues ∼710-805). Complementary structural analyses using X-ray crystallography, electron microscopy, and small-angle X-ray scattering of the Saccharomyces cerevisiae TREX-2 complex, expressed using Baculovirus-infected Sf9 cells, have indicated that the TPR-like repeats of the Sac3(M) region extend considerably further towards the N-terminus than previously thought, and also indicate that this region and Sac3(CID):Sus1:Cdc31 region of the S. cerevisiae complex are structurally independent. Although the density visible accounted for only ∼100kDa, a 5.3Å resolution cryo-EM reconstruction was obtained of the M-region of TREX-2 that showed an additional three putative α-helices extending towards the Sac3 N-terminus and these helices were also seen in a 4.9Å resolution structure obtained by X-ray crystallography. SUMMARY STATEMENT: We describe the expression, purification and structural characterization of the S. cerevisiae TREX-2 complex and demonstrate that the Sac3 TPR-like repeats are more extensive than ...SUMMARY STATEMENT: We describe the expression, purification and structural characterization of the S. cerevisiae TREX-2 complex and demonstrate that the Sac3 TPR-like repeats are more extensive than previously thought and that the M- and CID-regions do not appear to have a defined spatial orientation. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 369.1 KB | Display | ![]() |
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PDB format | ![]() | 292.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.6 KB | Display | ![]() |
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Full document | ![]() | 473.6 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3440C ![]() 5g5pC ![]() 3t5gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 149776.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SAC3, LEP1, YDR159W, YD8358.13 / Cell line (production host): Sf9 / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 52734.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: THP1, BUD29, YOL072W, O1140 / Cell line (production host): Sf9 / Production host: ![]() ![]() | ||
#3: Protein | Mass: 10397.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SEM1, DSH1, YDR363W-A / Cell line (production host): Sf9 / Production host: ![]() ![]() | ||
#4: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line (production host): Sf9 / Production host: ![]() ![]() #5: Protein/peptide | | Mass: 1039.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line (production host): Sf9 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Precipitant: 20% PEG 3350, 0.2 M Mg formate; protein 16.5 mg/ml in 0.3 M NaCl, 50 mM HEPES, pH 8, 5 mM DTT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 4.9→47.081 Å / Num. obs: 5268 / % possible obs: 98.7 % / Redundancy: 4.7 % / Net I/σ(I): 4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3T5G Resolution: 4.927→47.081 Å / SU ML: 0.91 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.927→47.081 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.9267→47.0828 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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