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- EMDB-64391: Structure of human TREX-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-64391
TitleStructure of human TREX-2
Map data
Sample
  • Cell: mRNA nuclear export, TREX-2, UAP56, gene regulation
    • Protein or peptide: Germinal-center associated nuclear protein
    • Protein or peptide: PCI domain-containing protein 2
    • Protein or peptide: 26S proteasome complex subunit SEM1
KeywordsmRNA nuclear export / TREX-2 / UAP56 / gene regulation
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsZhang X / Gong X / Ge X
Funding support China, 1 items
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, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64391.png

Downloads & links

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Map

FileDownload / File: emd_64391.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.187
Minimum - Maximum-0.8766612 - 1.0773584
Average (Standard dev.)-0.00030363668 (±0.025505427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64391_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64391_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64391_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : mRNA nuclear export, TREX-2, UAP56, gene regulation

EntireName: mRNA nuclear export, TREX-2, UAP56, gene regulation
Components
  • Cell: mRNA nuclear export, TREX-2, UAP56, gene regulation
    • Protein or peptide: Germinal-center associated nuclear protein
    • Protein or peptide: PCI domain-containing protein 2
    • Protein or peptide: 26S proteasome complex subunit SEM1

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Supramolecule #1: mRNA nuclear export, TREX-2, UAP56, gene regulation

SupramoleculeName: mRNA nuclear export, TREX-2, UAP56, gene regulation / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Germinal-center associated nuclear protein

MacromoleculeName: Germinal-center associated nuclear protein / type: protein_or_peptide / ID: 1 / Details: Twin Strep-GANP(580-1000) / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.891723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK GGGGSDEVDA AAEGSEGLGP CVLSLSTLIG TVAETSKEKY RLLDQRDRIM RQARVKRTD LDKARTFVGT CLDMCPEKER YMRETRSQLS VFEVVPGTDQ VDHAAAVKEY SRSSADQEEP LPHELRPLPV L SRTMDYLV ...String:
SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK GGGGSDEVDA AAEGSEGLGP CVLSLSTLIG TVAETSKEKY RLLDQRDRIM RQARVKRTD LDKARTFVGT CLDMCPEKER YMRETRSQLS VFEVVPGTDQ VDHAAAVKEY SRSSADQEEP LPHELRPLPV L SRTMDYLV TQIMDQKEGS LRDWYDFVWN RTRGIRKDIT QQHLCDPLTV SLIEKCTRFH IHCAHFMCEE PMSSFDAKIN NE NMTKCLQ SLKEMYQDLR NKGVFCASEA EFQGYNVLLS LNKGDILREV QQFHPAVRNS SEVKFAVQAF AALNSNNFVR FFK LVQSAS YLNACLLHCY FSQIRKDALR ALNFAYTVST QRSTIFPLDG VVRMLLFRDC EEATDFLTCH GLTVSDGCVE LNRS AFLEP EGLSKTRKSV FITRKLTVSV GEIVNGGPLP PVPRHTPVCS FNSQNKYIGE SLAAELPV

UniProtKB: Germinal-center associated nuclear protein

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Macromolecule #2: PCI domain-containing protein 2

MacromoleculeName: PCI domain-containing protein 2 / type: protein_or_peptide / ID: 2 / Details: 3XFlag-PCID2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.171941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDHDGDYK DHDIDYKDDD DKGSAAAMAH ITINQYLQQV YEAIDSRDGA SCAELVSFKH PHVANPRLQM ASPEEKCQQV LEPPYDEMF AAHLRCTYAV GNHDFIEAYK CQTVIVQSFL RAFQAHKEEN WALPVMYAVA LDLRVFANNA DQQLVKKGKS K VGDMLEKA ...String:
DYKDHDGDYK DHDIDYKDDD DKGSAAAMAH ITINQYLQQV YEAIDSRDGA SCAELVSFKH PHVANPRLQM ASPEEKCQQV LEPPYDEMF AAHLRCTYAV GNHDFIEAYK CQTVIVQSFL RAFQAHKEEN WALPVMYAVA LDLRVFANNA DQQLVKKGKS K VGDMLEKA AELLMSCFRV CASDTRAGIE DSKKWGMLFL VNQLFKIYFK INKLHLCKPL IRAIDSSNLK DDYSTAQRVT YK YYVGRKA MFDSDFKQAE EYLSFAFEHC HRSSQKNKRM ILIYLLPVKM LLGHMPTVEL LKKYHLMQFA EVTRAVSEGN LLL LHEALA KHEAFFIRCG IFLILEKLKI ITYRNLFKKV YLLLKTHQLS LDAFLVALKF MQVEDVDIDE VQCILANLIY MGHV KGYIS HQHQKLVVSK QNPFPPLSTV C

UniProtKB: PCI domain-containing protein 2

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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: Homo sapiens (human)
Molecular weightTheoretical: 8.284611 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSEKKQPVDL GLLEEDDEFE EFPAEDWAGL DEDEDAHVWE DNWDDDNVED DFSNQLRAEL EKHGYKMETS

UniProtKB: 26S proteasome complex subunit SEM1

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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: 7.9 / Details: 25 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 108904
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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