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- PDB-8u8c: Crystal structure of the TREX-2 complex in complex with the N-ter... -

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Basic information

Entry
Database: PDB / ID: 8u8c
TitleCrystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
Components
  • 26S proteasome complex subunit SEM1
  • ATP-dependent RNA helicase SUB2
  • Nuclear mRNA export protein SAC3
  • Nuclear mRNA export protein THP1
KeywordsRNA BINDING PROTEIN / mRNA binding protein
Function / homology
Function and homology information


actin filament-based process / transcription export complex / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / maintenance of DNA trinucleotide repeats / filamentous growth ...actin filament-based process / transcription export complex / cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex / mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / proteasome storage granule / proteasome assembly / subtelomeric heterochromatin formation / mRNA export from nucleus / transcription-coupled nucleotide-excision repair / protein folding chaperone / proteasome complex / protein export from nucleus / spliceosomal complex / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / mRNA splicing, via spliceosome / nuclear envelope / mitotic cell cycle / ribosomal small subunit biogenesis / ubiquitin-dependent protein catabolic process / double-stranded DNA binding / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / RNA helicase activity / regulation of cell cycle / RNA helicase / mRNA binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 ...Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
26S proteasome complex subunit SEM1 / Nuclear mRNA export protein SAC3 / ATP-dependent RNA helicase SUB2 / Nuclear mRNA export protein THP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXie, Y. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133743 United States
CitationJournal: To Be Published
Title: Structural mechanism of mRNP remodeling
Authors: Xie, Y. / Ren, Y.
History
DepositionSep 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: ATP-dependent RNA helicase SUB2


Theoretical massNumber of molelcules
Total (without water)126,6094
Polymers126,6094
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-61 kcal/mol
Surface area40560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.861, 87.001, 169.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Nuclear mRNA export protein SAC3


Mass: 57800.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SAC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46674
#2: Protein Nuclear mRNA export protein THP1


Mass: 52734.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: THP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08231
#3: Protein 26S proteasome complex subunit SEM1


Mass: 10397.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SEM1 / Production host: Escherichia coli (E. coli) / References: UniProt: O94742
#4: Protein ATP-dependent RNA helicase SUB2


Mass: 5676.751 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SUB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07478
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.5, and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0081 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. obs: 73285 / % possible obs: 94.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 32.17 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 2178 / Rpim(I) all: 0.218

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.36 Å / SU ML: 0.2601 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 3398 4.67 %
Rwork0.1912 69380 -
obs0.193 72778 82.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.93 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 0 75 7881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257976
X-RAY DIFFRACTIONf_angle_d0.463710790
X-RAY DIFFRACTIONf_chiral_restr0.03651193
X-RAY DIFFRACTIONf_plane_restr0.00411390
X-RAY DIFFRACTIONf_dihedral_angle_d4.19911029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.2616970.25051934X-RAY DIFFRACTION55.45
2.43-2.470.3175970.24012030X-RAY DIFFRACTION58.35
2.47-2.510.30591100.23652131X-RAY DIFFRACTION60.85
2.51-2.550.29691160.23032333X-RAY DIFFRACTION65.18
2.55-2.590.29281230.22482325X-RAY DIFFRACTION68.67
2.59-2.640.28071220.22512583X-RAY DIFFRACTION72.77
2.64-2.690.24381370.22192684X-RAY DIFFRACTION76.51
2.69-2.750.27221350.21642822X-RAY DIFFRACTION80.62
2.75-2.810.28571400.21833004X-RAY DIFFRACTION85.13
2.81-2.870.25561460.22243029X-RAY DIFFRACTION87.15
2.87-2.940.2781480.24083129X-RAY DIFFRACTION88.78
2.94-3.020.32461560.23593152X-RAY DIFFRACTION89.87
3.02-3.110.25291580.23593162X-RAY DIFFRACTION90.49
3.11-3.210.29111580.22183142X-RAY DIFFRACTION90.63
3.21-3.330.23561550.20863232X-RAY DIFFRACTION91.64
3.33-3.460.24291650.20493227X-RAY DIFFRACTION91.48
3.46-3.620.23241540.19013201X-RAY DIFFRACTION91.49
3.62-3.810.25681550.17793173X-RAY DIFFRACTION91
3.81-4.050.22041500.16463117X-RAY DIFFRACTION89.07
4.05-4.360.15341500.15643137X-RAY DIFFRACTION88.65
4.36-4.790.19181600.15223190X-RAY DIFFRACTION92.31
4.79-5.480.17681500.16523256X-RAY DIFFRACTION92.4
5.48-6.890.21141550.19053216X-RAY DIFFRACTION91.65
6.9-29.360.17181610.14923171X-RAY DIFFRACTION90.59

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