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- PDB-9upc: Structure of human TREX-2 -

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Basic information

Entry
Database: PDB / ID: 9upc
TitleStructure of human TREX-2
Components
  • 26S proteasome complex subunit SEM1
  • Germinal-center associated nuclear protein
  • PCI domain-containing protein 2
KeywordsGENE REGULATION / mRNA nuclear export / TREX-2 / UAP56
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 / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear pore nuclear basket / histone H3 acetyltransferase activity / integrator complex / nucleosome organization / 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 / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear pore nuclear basket / histone H3 acetyltransferase activity / integrator complex / nucleosome organization / proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / positive regulation of B cell differentiation / 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) / Somitogenesis / Resolution of D-loop Structures through Holliday Junction Intermediates / poly(A)+ mRNA export from nucleus / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression, epigenetic / histone acetyltransferase activity / Presynaptic phase of homologous DNA pairing and strand exchange / proteasome assembly / mRNA export from nucleus / somatic hypermutation of immunoglobulin genes / histone acetyltransferase / spleen development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / transcription elongation by RNA polymerase II / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / 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 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / double-strand break repair via homologous recombination / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / HDR through Homologous Recombination (HRR) / CDK-mediated phosphorylation and removal of Cdc6 / 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 RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / UCH proteinases / KEAP1-NFE2L2 pathway / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / protein transport / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / double-stranded DNA binding / histone binding / nuclear membrane / nucleic acid binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / chromatin binding
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 / MCM3AP domain of GANP / 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 / MCM3AP domain of GANP / 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: 3.14 Å
AuthorsZhang, X. / Gong, X. / Ge, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471302 China
CitationJournal: To Be Published
Title: Structure of human TREX-2
Authors: Zhang, X. / Gong, X. / Ge, X.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)109,3483
Polymers109,3483
Non-polymers00
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 Germinal-center associated nuclear protein / GANP / 80 kDa MCM3-associated protein / MCM3 acetylating protein / MCM3AP / MCM3 acetyltransferase


Mass: 51891.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Twin Strep-GANP(580-1000) / Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3AP, GANP, KIAA0572, MAP80 / Production host: Homo sapiens (human)
References: UniProt: O60318, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein PCI domain-containing protein 2 / CSN12-like protein


Mass: 49171.941 Da / Num. of mol.: 1 / Fragment: 3XFlag-PCID2
Source method: isolated from a genetically manipulated source
Details: 3XFlag-PCID2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PCID2, HT004 / Production host: Homo sapiens (human) / 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 / Production host: Homo sapiens (human) / References: UniProt: P60896
Has protein modificationN

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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: mRNA nuclear export, TREX-2, UAP56, gene regulation / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9 / Details: 25 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC4.63D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108904 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036294
ELECTRON MICROSCOPYf_angle_d0.5168501
ELECTRON MICROSCOPYf_dihedral_angle_d14.9422341
ELECTRON MICROSCOPYf_chiral_restr0.034935
ELECTRON MICROSCOPYf_plane_restr0.0041095

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