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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 / maintenance of DNA trinucleotide repeats / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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 / maintenance of DNA trinucleotide repeats / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / filamentous growth / proteasome regulatory particle, lid subcomplex / mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / proteasome storage granule / mRNA export from nucleus / proteasome assembly / subtelomeric heterochromatin formation / 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 / double-stranded DNA binding / ubiquitin-dependent protein catabolic process / 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 / cytoplasm / cytosol
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: Structure / Year: 2025
Title: Structures and mRNP remodeling mechanism of the TREX-2 complex.
Authors: Yihu Xie / Bradley P Clarke / Dongqi Xie / Menghan Mei / Prasanna Bhat / Pate S Hill / Alexia E Angelos / Tolga Çağatay / Mariam Haider / Scott E Collier / Melissa G Chambers / Vasilisa ...Authors: Yihu Xie / Bradley P Clarke / Dongqi Xie / Menghan Mei / Prasanna Bhat / Pate S Hill / Alexia E Angelos / Tolga Çağatay / Mariam Haider / Scott E Collier / Melissa G Chambers / Vasilisa Aksenova / Mary Dasso / Beatriz M A Fontoura / Yi Ren /
Abstract: mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before ...mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before export to the cytoplasm, mRNPs undergo dynamic remodeling governed by the DEAD-box helicase DDX39B (yeast Sub2). DDX39B/Sub2 primarily functions in the nucleus and leaves the mRNP prior to export through the nuclear pore complex; however, the underlying mechanisms remain elusive. Here, we identify the conserved TREX-2 complex as the long-sought factor that facilitates DDX39B/Sub2 to complete the mRNP remodeling cycle. Our crystallographic and cryoelectron microscopy (cryo-EM) analyses demonstrate that TREX-2 modulates the activities of DDX39B/Sub2 through multiple interactions. Critically, a conserved "trigger loop" from TREX-2 splits the two RecA domains of DDX39B/Sub2 and promotes the removal of DDX39B/Sub2 from mRNP. Our findings suggest that TREX-2 coordinates with DDX39B/Sub2 and the human export receptor NXF1-NXT1 (yeast Mex67-Mtr2) to complete the final steps of nuclear mRNP assembly.
History
DepositionSep 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: 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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