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- EMDB-74098: Conserved mRNP remodeling mechanism of the TREX-2L (Thp3/Csn12/Se... -

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Basic information

Entry
Database: EMDB / ID: EMD-74098
TitleConserved mRNP remodeling mechanism of the TREX-2L (Thp3/Csn12/Sem1) complex
Map data
Sample
  • Complex: TREX-2 like complex (TREX-2L)
    • Protein or peptide: Protein THP3
    • Protein or peptide: Cop9 signalosome complex subunit 12
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: ATP-dependent RNA helicase SUB2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsTREX-2 / TREX-2 like / Sub2 / mRNA nuclear export / RNA BINDING PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsAngelos AE / Clarke BP / Xie Y / Ren Y
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74098.png

Downloads & links

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Map

FileDownload / File: emd_74098.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 236.736 Å		0.82 Å/pix.
x 288 pix.
= 236.736 Å		0.82 Å/pix.
x 288 pix.
= 236.736 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.105659164 - 0.18276416
Average (Standard dev.)0.00010041404 (±0.004245573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 236.73601 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74098_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74098_half_map_2.map
Projections & Slices
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Sample components

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Entire : TREX-2 like complex (TREX-2L)

EntireName: TREX-2 like complex (TREX-2L)
Components
  • Complex: TREX-2 like complex (TREX-2L)
    • Protein or peptide: Protein THP3
    • Protein or peptide: Cop9 signalosome complex subunit 12
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: ATP-dependent RNA helicase SUB2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: TREX-2 like complex (TREX-2L)

SupramoleculeName: TREX-2 like complex (TREX-2L) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Protein THP3

MacromoleculeName: Protein THP3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.251906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSDELER RKRRAERFSQ GPSATTNSND NLNEDFANLN AISSKSHQYD KKIHVVGRCQ TLEKSYLRLT SEPNPDLIRP PNILQKMYC LLMDKYQSKT ATYTYLCDQF KSMRQDLRVQ MIENSFTIKV YQTHARIALE NGDLGEFNQC QNRIMALFEN P TIPKKSYS ...String:
GAMGSDELER RKRRAERFSQ GPSATTNSND NLNEDFANLN AISSKSHQYD KKIHVVGRCQ TLEKSYLRLT SEPNPDLIRP PNILQKMYC LLMDKYQSKT ATYTYLCDQF KSMRQDLRVQ MIENSFTIKV YQTHARIALE NGDLGEFNQC QNRIMALFEN P TIPKKSYS EFICYSVLYS MLTEDYPSIS HLKLKLIDDG SSEILEDEHV KMIFELSDMK LVGNYHYFMK NYLKLHKFEK CL INSFLNL EKLIFLTIIC KSYNQVNLDF VKSEFNFNSI EETTNFLNEQ NLTEFILNKQ ITDSNGKSSN IKILNTKGCR VQL IQNYMK SKKIDIKGQK

UniProtKB: Protein THP3

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Macromolecule #2: Cop9 signalosome complex subunit 12

MacromoleculeName: Cop9 signalosome complex subunit 12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.099902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GADPNSMDVD IGCYFEEKRY DDKLLDFIRY DVKTPKKTKY ILQRPTATDE ESVRLQRFYQ LGVDLKLKYS KRRSLKKQGR IKNATEELL RLANEQLKLF NRIVERETNW IIYPLWVMAK QLIRLANESS ELNKDSIEEC GRTIHRSFTI CLNDRNPRLN E NKKIGCYM ...String:
GADPNSMDVD IGCYFEEKRY DDKLLDFIRY DVKTPKKTKY ILQRPTATDE ESVRLQRFYQ LGVDLKLKYS KRRSLKKQGR IKNATEELL RLANEQLKLF NRIVERETNW IIYPLWVMAK QLIRLANESS ELNKDSIEEC GRTIHRSFTI CLNDRNPRLN E NKKIGCYM FANLEFSIYH RLSNKDMIKN LVKVLESRVN ARDIPPLNKS LAMEHKSQVV LYNYYLGQYY GCLENDHERG FF HLNEALL QCPMLYVEST GKFVLQGQME KIMILLVPLA LLTKRLYPHW DHPVIAGVIT RSKRLSQVYP TLVRSVISGN LSL YEATAA SHERFFLSQG LHVVITLLRE VVFTRLVQRC WQWGNDRKSI MPLKILLATK QHDSSANEDE EEQLDALECR LASA IASGL LRAYLSHSNR CIVFSKKEPF PHSK

UniProtKB: Cop9 signalosome complex subunit 12

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Macromolecule #3: 26S proteasome complex subunit SEM1

MacromoleculeName: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.827621 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADLMSTDVA AAQAQSKIDL TKKKNEEINK KSLEEDDEFE DFPIDTWANG ETIKSNAVTQ TNIWEENWDD VEVDDDFTNE LKAELDRYK RENQ

UniProtKB: 26S proteasome complex subunit SEM1

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Macromolecule #4: ATP-dependent RNA helicase SUB2

MacromoleculeName: ATP-dependent RNA helicase SUB2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.901523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSMSHEG EEDLLEYSDN EQEIQIDASK AAEAGETGAA TSATEGDNNN NTAAGDKKGS YVGIHSTGFK DFLLKPELSR AIIDCGFEH PSEVQQHTIP QSIHGTDVLC QAKSGLGKTA VFVLSTLQQL (A1AMM)PVPGEVAVV VICNARELAY QIRNE YLRF ...String:
GAMGSMSHEG EEDLLEYSDN EQEIQIDASK AAEAGETGAA TSATEGDNNN NTAAGDKKGS YVGIHSTGFK DFLLKPELSR AIIDCGFEH PSEVQQHTIP QSIHGTDVLC QAKSGLGKTA VFVLSTLQQL (A1AMM)PVPGEVAVV VICNARELAY QIRNE YLRF SKYMPDVKTA VFYGGTPISK DAELLKNKDT APHIVVATPG RLKALVREKY IDLSHVKNFV IDECDKVLEE LDMRRD VQE IFRATPRDKQ VMMFSATLSQ EIRPICRRFL QNPLEIFVDD EAKLTLHGLQ QYYIKLEERE KNRKLAQLLD DLEFNQV II FVKSTTRANE LTKLLNASNF PAITVHGHMK QEERIARYKA FKDFEKRICV STDVFGRGID IERINLAINY DLTNEADQ Y LHRVGRAGRF GTKGLAISFV SSKEDEEVLA KIQERFDVKI AEFPEEGIDP STYLNN

UniProtKB: ATP-dependent RNA helicase SUB2

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 57575
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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