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- PDB-4trq: Crystal structure of Sac3/Thp1/Sem1 -

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Basic information

Entry
Database: PDB / ID: 4trq
TitleCrystal structure of Sac3/Thp1/Sem1
Components
  • 26S proteasome complex subunit SEM1Proteasome
  • Nuclear mRNA export protein SAC3
  • Nuclear mRNA export protein THP1
KeywordsGENE REGULATION / PCI domain / TREX-2 / gene expression
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
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
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 / molecular replacement / Resolution: 3.1 Å
AuthorsHellerschmied, D. / Schneider, S. / Kohler, A. / Clausen, T.
CitationJournal: Cell / Year: 2015
Title: The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.
Authors: Schneider, M. / Hellerschmied, D. / Schubert, T. / Amlacher, S. / Vinayachandran, V. / Reja, R. / Pugh, B.F. / Clausen, T. / Kohler, A.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Nuclear mRNA export protein SAC3
E: Nuclear mRNA export protein THP1
F: 26S proteasome complex subunit SEM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7727
Polymers151,6766
Non-polymers961
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19880 Å2
ΔGint-107 kcal/mol
Surface area55190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.741, 125.741, 268.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

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


Mass: 35173.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SAC3, LEP1, YDR159W, YD8358.13 / Plasmid: pST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL / References: UniProt: P46674
#2: Protein Nuclear mRNA export protein THP1 / Bud site selection protein 29


Mass: 33446.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: THP1, BUD29, YOL072W, O1140 / Plasmid: pST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL / References: UniProt: Q08231
#3: Protein 26S proteasome complex subunit SEM1 / Proteasome


Mass: 7218.448 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SEM1, DSH1, YDR363W-A / Plasmid: pST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL / References: UniProt: O94742
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.5M Li2SO4, 10% PEG-8.000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→47.608 Å / Num. all: 39394 / Num. obs: 39394 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 75.91 Å2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.13 / Rsym value: 0.115 / Net I/av σ(I): 6.4 / Net I/σ(I): 10.4 / Num. measured all: 172622
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.274.60.74312609557200.3850.743299.9
3.27-3.474.50.4451.72401253930.2320.4453.299.7
3.47-3.714.30.3212.42183750450.1690.3214.498.6
3.71-44.40.1953.92081947130.1020.1957.399.6
4-4.384.40.1116.81942543820.0580.11111.999.7
4.38-4.94.30.0858.81680139170.0450.08514.898
4.9-5.664.40.0779.61567635330.040.07715.599
5.66-6.934.30.07210.31277029840.0380.07215.598.4
6.93-9.84.20.03618.3994623550.0190.03626.998.1
9.8-47.6083.90.02425.3524113520.0130.0243896.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
Omodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3t5v

3t5v


Resolution: 3.1→47.608 Å / FOM work R set: 0.8213 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1976 5.02 %
Rwork0.1939 37390 -
obs0.1962 39366 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.6 Å2 / Biso mean: 76.13 Å2 / Biso min: 22.09 Å2
Refinement stepCycle: final / Resolution: 3.1→47.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10516 0 5 0 10521
Biso mean--94.62 --
Num. residues----1268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810756
X-RAY DIFFRACTIONf_angle_d1.27114580
X-RAY DIFFRACTIONf_chiral_restr0.0481618
X-RAY DIFFRACTIONf_plane_restr0.0071874
X-RAY DIFFRACTIONf_dihedral_angle_d17.5424060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.17750.31941490.291326552804100
3.1775-3.26340.32371490.276726352784100
3.2634-3.35940.31181460.248526482794100
3.3594-3.46780.29981260.23862649277599
3.4678-3.59170.28441300.23522601273197
3.5917-3.73550.31831360.24412657279399
3.7355-3.90540.23071410.18942668280999
3.9054-4.11120.21351250.17222680280599
4.1112-4.36860.20451520.14952664281699
4.3686-4.70570.18091190.14082640275997
4.7057-5.17870.19261390.15092683282298
5.1787-5.92690.23621650.18482681284699
5.9269-7.46260.22111440.21382714285897
7.4626-47.61370.22461550.18862815297096
Refinement TLS params.Method: refined / Origin x: -61.6522 Å / Origin y: -2.4597 Å / Origin z: 44.9741 Å
111213212223313233
T0.392 Å2-0.0235 Å20.0985 Å2-0.2408 Å2-0.0153 Å2--0.2716 Å2
L0.3786 °2-0.1613 °2-0.0974 °2-0.1767 °20.2052 °2--0.271 °2
S-0.0239 Å °-0.0288 Å °-0.0188 Å °0.087 Å °-0.0489 Å °-0.0155 Å °0.0983 Å °-0.1358 Å °-0.0181 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA253 - 551
2X-RAY DIFFRACTION1allB170 - 455
3X-RAY DIFFRACTION1allC30 - 89
4X-RAY DIFFRACTION1allD253 - 551
5X-RAY DIFFRACTION1allE170 - 455
6X-RAY DIFFRACTION1allF30 - 89
7X-RAY DIFFRACTION1all7027

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