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- PDB-9zeb: Cryo-EM structure of the TREX-2.1 complex (Thp3/Csn12/Sem1) bound... -

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Basic information

Entry
Database: PDB / ID: 9zeb
TitleCryo-EM structure of the TREX-2.1 complex (Thp3/Csn12/Sem1) bound to the DEAD-box ATPase Sub2
Components
  • 26S proteasome complex subunit SEM1
  • ATP-dependent RNA helicase SUB2
  • Cop9 signalosome complex subunit 12
  • Protein THP3
KeywordsRNA BINDING PROTEIN / TREX-2 / TREX-2 like / Sub2 / mRNA nuclear export
Function / homology
Function and homology information


: / cellular response to pheromone / conjugation with cellular fusion / transcription export complex / SAGA complex localization to transcription regulatory region / maintenance of DNA trinucleotide repeats / regulation of protein neddylation / filamentous growth / COP9 signalosome / mRNA 3'-end processing ...: / cellular response to pheromone / conjugation with cellular fusion / transcription export complex / SAGA complex localization to transcription regulatory region / maintenance of DNA trinucleotide repeats / regulation of protein neddylation / filamentous growth / COP9 signalosome / mRNA 3'-end processing / U2-type prespliceosome assembly / transcription export complex 2 / proteasome regulatory particle, lid subcomplex / subtelomeric heterochromatin formation / proteasome storage granule / proteasome assembly / mRNA export from nucleus / proteasome complex / protein folding chaperone / transcription-coupled nucleotide-excision repair / mRNA splicing, via spliceosome / double-strand break repair via homologous recombination / euchromatin / transcription elongation by RNA polymerase II / double-stranded DNA binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / regulation of cell cycle / chromosome, telomeric region / RNA helicase activity / RNA helicase / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA-templated transcription / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. ...Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / PCI domain / Proteasome component (PCI) domain / PCI domain 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 26S proteasome complex subunit SEM1 / Cop9 signalosome complex subunit 12 / ATP-dependent RNA helicase SUB2 / Protein THP3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsAngelos, A.E. / Clarke, B.P. / Xie, Y. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Conserved mRNP remodeling mechanism of the TREX-2.1 complex.
Authors: Alexia E Angelos / Ryuta Asada / Bradley P Clarke / Pate S Hill / Lydia Li / Menghan Mei / Jalen L Smith / Ethan R Xie / Walter C Reter / Samuel J Smithee / Yihu Xie / Ben Montpetit / Yi Ren /
Abstract: Processing, packaging, and nuclear export of messenger ribonucleoprotein particles (mRNPs) are critical for eukaryotic gene expression, with the DEAD-box ATPase DDX39B (yeast Sub2) playing a central ...Processing, packaging, and nuclear export of messenger ribonucleoprotein particles (mRNPs) are critical for eukaryotic gene expression, with the DEAD-box ATPase DDX39B (yeast Sub2) playing a central role in mRNP processing and remodeling. Our recent studies identified human TREX-2 (GANP•PCID2•DSS1), yeast TREX-2 (Sac3•Thp1•Sem1), and a related human TREX-2.1 complex (LENG8•PCID2•DSS1) as key regulators of DDX39B/Sub2. Here, we characterize the yeast TREX-2.1 (scTREX-2.1) complex, composed of Thp3, Csn12, and Sem1. We show that the scTREX-2.1 complex directly interacts with Sub2 and co-occupies a fraction of CBC-containing mRNPs with Sub2. Using cryo-electron microscopy , we determined the structure of scTREX-2.1 bound to Sub2, revealing a conserved "trigger loop" mechanism by which scTREX-2.1 regulates Sub2 activity. Functional assays show that disruption of scTREX-2.1 leads to the accumulation of intron-containing pre-mRNAs. These findings uncover a conserved mechanism from yeast to humans by which TREX-2 and TREX-2.1 complexes regulate Sub2/DDX39B during nuclear mRNP maturation, providing insights into the coordination of mRNP remodeling and processing prior to nuclear export.
History
DepositionNov 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein THP3
B: Cop9 signalosome complex subunit 12
C: 26S proteasome complex subunit SEM1
D: ATP-dependent RNA helicase SUB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5085
Polymers151,0814
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein THP3 / THO-related protein 3


Mass: 39251.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THP3, YPR045C, YP9499.03c / Production host: Escherichia coli (E. coli) / References: UniProt: Q12049
#2: Protein Cop9 signalosome complex subunit 12


Mass: 50099.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSN12, YJR084W, J1860 / Production host: Escherichia coli (E. coli) / References: UniProt: P47130
#3: Protein 26S proteasome complex subunit SEM1


Mass: 10827.621 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 / Production host: Escherichia coli (E. coli) / References: UniProt: O94742
#4: Protein ATP-dependent RNA helicase SUB2 / Suppressor of BRR1 protein 2


Mass: 50901.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUB2, YDL084W / Production host: Escherichia coli (E. coli) / References: UniProt: Q07478, RNA helicase
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TREX-2 like complex (TREX-2L) / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 57.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57575 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 175.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00297928
ELECTRON MICROSCOPYf_angle_d0.520310704
ELECTRON MICROSCOPYf_chiral_restr0.03891195
ELECTRON MICROSCOPYf_plane_restr0.00351364
ELECTRON MICROSCOPYf_dihedral_angle_d5.4291045

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