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- PDB-8r7j: Cryo-EM structure of the human TREX-2 complex -

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Basic information

Entry
Database: PDB / ID: 8r7j
TitleCryo-EM structure of the human TREX-2 complex
Components
  • 26S proteasome complex subunit SEM1
  • Germinal-center associated nuclear protein
  • PCI domain-containing protein 2
KeywordsGENE REGULATION / mRNA export / nuclear pore basket
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone H3 acetyltransferase activity / nuclear pore nuclear basket / nucleosome organization / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / integrator complex / proteasome regulatory particle, lid subcomplex ...negative regulation of lymphoid progenitor cell differentiation / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone H3 acetyltransferase activity / nuclear pore nuclear basket / nucleosome organization / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / integrator complex / proteasome regulatory particle, lid subcomplex / positive regulation of B cell differentiation / poly(A)+ mRNA export from nucleus / cellular response to type I interferon / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / histone acetyltransferase activity / Cross-presentation of soluble exogenous antigens (endosomes) / negative regulation of gene expression, epigenetic / Somitogenesis / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / spleen development / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / somatic hypermutation of immunoglobulin genes / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / histone acetyltransferase / proteasome assembly / mRNA export from nucleus / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SPOP-mediated proteasomal degradation of PD-L1(CD274) / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / proteasome complex / regulation of proteasomal protein catabolic process / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / proteasomal protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / transcription elongation by RNA polymerase II / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / HDR through Homologous Recombination (HRR) / CDK-mediated phosphorylation and removal of Cdc6 / ABC-family protein mediated transport / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Regulation of RAS by GAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / UCH proteinases / KEAP1-NFE2L2 pathway / Downstream TCR signaling / synaptic vesicle / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / protein transport
Similarity search - Function
Germinal-centre associated nuclear protein, MCM3AP domain / Germinal-centre associated nuclear protein, nucleoporin homology domain / Germinal-centre associated nuclear protein, CID domain / MCM3AP, RNA recognition motif / Binding region of GANP to ENY2 / Nucleoporin homology of Germinal-centre associated nuclear protein / GANP, MCM3AP N-terminal domain / Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 ...Germinal-centre associated nuclear protein, MCM3AP domain / Germinal-centre associated nuclear protein, nucleoporin homology domain / Germinal-centre associated nuclear protein, CID domain / MCM3AP, RNA recognition motif / Binding region of GANP to ENY2 / Nucleoporin homology of Germinal-centre associated nuclear protein / GANP, MCM3AP N-terminal 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-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Germinal-center associated nuclear protein / 26S proteasome complex subunit SEM1 / PCI domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHohmann, U. / Graf, M. / Plaschka, C.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
H2020 Marie Curie Actions of the European Commission896416European Union
European Molecular Biology Organization (EMBO)ALTF_1175-2019European Union
CitationJournal: Nature / Year: 2026
Title: An ATP-gated molecular switch orchestrates human mRNA export.
Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alexander W Phillips / Daria Riabov-Bassat / Rupert Faraway / Thomas ...Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alexander W Phillips / Daria Riabov-Bassat / Rupert Faraway / Thomas Pühringer / Michael-Florian Szalay / Elisabeth Roitinger / Julius Brennecke / Clemens Plaschka /
Abstract: The nuclear export of mRNA is an important step in eukaryotic gene expression. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein complexes (mRNPs) ...The nuclear export of mRNA is an important step in eukaryotic gene expression. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein complexes (mRNPs), the subsequent events that govern mRNA export are poorly understood. Here we uncover the molecular basis underlying key events of human mRNA export, including the remodelling of mRNP-bound transcription-export complexes (TREX), the formation of export-competent mRNPs, the docking of mRNPs at the nuclear pore complex (NPC), and the release of mRNPs at the NPC to initiate their export. Our biochemical and structural data show that the ATPase UAP56 (also known as DDX39) acts as a central molecular switch that directs nucleoplasmic mRNPs from TREX to NPC-anchored TREX-2 complexes through its ATP-gated mRNA-binding cycle. Collectively, these findings establish a mechanistic framework for a general and evolutionarily conserved mRNA export pathway.
History
DepositionNov 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Germinal-center associated nuclear protein
B: PCI domain-containing protein 2
C: 26S proteasome complex subunit SEM1


Theoretical massNumber of molelcules
Total (without water)102,5413
Polymers102,5413
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Germinal-center associated nuclear protein / GANP / 80 kDa MCM3-associated protein / MCM3 acetylating protein / MCM3AP / MCM3 acetyltransferase


Mass: 48160.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3AP, GANP, KIAA0572, MAP80 / Plasmid: plasmid 408 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 RIL
References: UniProt: O60318, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein PCI domain-containing protein 2 / CSN12-like protein


Mass: 46095.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCID2, HT004 / Plasmid: plasmid 484 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q5JVF3
#3: Protein 26S proteasome complex subunit SEM1 / 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot ...26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEM1, C7orf76, DSS1, SHFDG1, SHFM1 / Plasmid: plasmid 484 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P60896
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: Human TREX-2 complex middle domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.9
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 316490 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066173
ELECTRON MICROSCOPYf_angle_d1.3028343
ELECTRON MICROSCOPYf_dihedral_angle_d6.702810
ELECTRON MICROSCOPYf_chiral_restr0.063926
ELECTRON MICROSCOPYf_plane_restr0.0091071

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