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- PDB-5l3t: Structure of the Saccharomyces cerevisiae TREX-2 complex -

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Basic information

Entry
Database: PDB / ID: 5l3t
TitleStructure of the Saccharomyces cerevisiae TREX-2 complex
Components
  • (Sac3polyAla) x 2
  • 26S proteasome complex subunit SEM1Proteasome
  • Nuclear mRNA export protein SAC3
  • Nuclear mRNA export protein THP1
KeywordsTRANSPORT PROTEIN / nuclear export / TREX-2 complex / Sac3 / Thp1
Function / homology
Function and homology information


actin filament-based process / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / maintenance of DNA trinucleotide repeats / 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 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / maintenance of DNA trinucleotide repeats / filamentous growth / mRNA 3'-end processing / proteasome regulatory particle, lid subcomplex / poly(A)+ mRNA export from nucleus / proteasome storage granule / transcription-coupled nucleotide-excision repair / proteasome assembly / 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 / ribosomal small subunit biogenesis / mitotic cell cycle / nuclear envelope / 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 / cytosol / cytoplasm
Similarity search - Function
Csn12 family / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 ...Csn12 family / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain / PCI domain profile.
Similarity search - Domain/homology
26S proteasome complex subunit SEM1 / Nuclear mRNA export protein SAC3 / Nuclear mRNA export protein THP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.927 Å
AuthorsStewart, M. / Aibara, S.
CitationJournal: J Struct Biol / Year: 2016
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.
History
DepositionMay 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity / entity_src_gen
Item: _citation.journal_abbrev / _entity.formula_weight ..._citation.journal_abbrev / _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.3Oct 16, 2019Group: Data collection / Structure summary / Category: entity / reflns_shell / Item: _entity.formula_weight
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear mRNA export protein SAC3
B: Nuclear mRNA export protein THP1
C: 26S proteasome complex subunit SEM1
D: Sac3polyAla
E: Sac3polyAla
F: Sac3polyAla


Theoretical massNumber of molelcules
Total (without water)218,0696
Polymers218,0696
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-46 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.170, 84.090, 165.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear mRNA export protein SAC3 / Leucine permease transcriptional regulator


Mass: 149776.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SAC3, LEP1, YDR159W, YD8358.13 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P46674
#2: Protein Nuclear mRNA export protein THP1 / Bud site selection protein 29


Mass: 52734.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THP1, BUD29, YOL072W, O1140 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08231
#3: Protein 26S proteasome complex subunit SEM1 / Proteasome


Mass: 10397.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEM1, DSH1, YDR363W-A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94742
#4: Protein/peptide Sac3polyAla


Mass: 2060.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#5: Protein/peptide Sac3polyAla


Mass: 1039.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 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

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimless0.5.17data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

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
RfactorNum. reflection% reflection
Rfree0.3701 173 5.73 %
Rwork0.3378 --
obs0.3395 3017 57.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.927→47.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 0 0 6831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036979
X-RAY DIFFRACTIONf_angle_d0.579466
X-RAY DIFFRACTIONf_dihedral_angle_d15.0852573
X-RAY DIFFRACTIONf_chiral_restr0.041066
X-RAY DIFFRACTIONf_plane_restr0.0051220
LS refinement shellResolution: 4.9267→47.0828 Å
RfactorNum. reflection% reflection
Rfree0.3701 173 -
Rwork0.3378 2844 -
obs--57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34320.3022-0.07060.13580.04150.3639-0.38880.65440.0429-0.8422-0.54690.20620.1068-0.5934-0.0590.4396-0.0782-0.2020.54150.1832-0.009529.2883-24.5792-28.8292
21.29240.7725-0.0850.28720.12420.45050.19590.1929-0.2128-0.2784-0.55660.6767-0.3966-0.2381-0.02630.18440.1137-0.23670.23960.32020.51076.6099-16.6468-6.8714
30.7480.3402-0.13840.2267-0.30630.73470.68510.1488-0.5141-0.1718-0.3372-0.0102-0.0418-0.0550.53670.80730.0709-0.21970.6330.7170.4053-6.3996-30.8823-23.0145
41.5133-1.2426-0.67851.0070.5650.9194-0.01270.0462-0.0823-0.08040.0717-0.01550.00310.02130.24140.4049-0.6172-0.09660.1860.31230.097860.32347.6335-25.2679
50.03050.02540.02920.01820.04690.040.08390.1094-0.08780.26790.1187-0.1264-0.23060.1078-0.02490.26210.1172-0.09170.3895-0.11790.361661.60483.7254-16.1264
6-0.0005-0.0044-0.00230.01580.01420.01190.02380.09330.21-0.01180.10460.1862-0.0355-0.13390.00430.94740.2154-0.50840.26290.0150.648852.96020.0149-24.1698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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