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- EMDB-64390: Structure of the human TREX-2 bound to UAP56 -

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Basic information

Entry
Database: EMDB / ID: EMD-64390
TitleStructure of the human TREX-2 bound to UAP56
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
    • Protein or peptide: Spliceosome RNA helicase DDX39B
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsmRNA nuclear export / TREX-2 / UAP56 / gene regulation
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / transcription export complex / U6 snRNP / 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 ...negative regulation of lymphoid progenitor cell differentiation / transcription export complex / U6 snRNP / 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 / ATP-dependent activity, acting on RNA / mRNA 3'-end processing / ATP-dependent protein binding / U4 snRNA binding / proteasome regulatory particle, lid subcomplex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / Regulation of ornithine decarboxylase (ODC) / U4 snRNP / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / positive regulation of B cell differentiation / 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) / poly(A)+ mRNA export from nucleus / Resolution of D-loop Structures through Holliday Junction Intermediates / negative regulation of gene expression, epigenetic / Impaired BRCA2 binding to RAD51 / spliceosomal complex assembly / histone acetyltransferase activity / Presynaptic phase of homologous DNA pairing and strand exchange / U6 snRNA binding / proteasome assembly / RHOBTB2 GTPase cycle / mRNA export from nucleus / somatic hypermutation of immunoglobulin genes / histone acetyltransferase / spleen development / mRNA Splicing - Major Pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / proteasome complex / RNA splicing / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / spliceosomal complex / 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 / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / 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 / mRNA splicing, via spliceosome / 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 / double-strand break repair via homologous recombination / 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 / 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
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 / RNA helicase, DEAD-box type, Q motif / PCI domain / DEAD-box RNA helicase Q motif profile. / Proteasome component (PCI) domain / PCI domain profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / 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
Germinal-center associated nuclear protein / 26S proteasome complex subunit SEM1 / Spliceosome RNA helicase DDX39B / PCI domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 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 the human TREX-2 bound to UAP56
Authors: Zhang X / Gong X / Ge X
History
DepositionApr 28, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64390.png

Downloads & links

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Map

FileDownload / File: emd_64390.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

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-0.38584724 - 0.6494947
Average (Standard dev.)-0.00003504565 (±0.01854708)
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_64390_msk_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_64390_half_map_1.map
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Half map: #1

Fileemd_64390_half_map_2.map
Projections & Slices
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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
    • Protein or peptide: Spliceosome RNA helicase DDX39B
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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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: #1-#4
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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Macromolecule #4: Spliceosome RNA helicase DDX39B

MacromoleculeName: Spliceosome RNA helicase DDX39B / type: protein_or_peptide / ID: 4 / Details: 3XFlag-UAP56 (DDX39B) / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.132312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDHDGDYK DHDIDYKDDD DKGSAAAMAE NDVDNELLDY EDDEVETAAG GDGAEAPAKK DVKGSYVSIH SSGFRDFLLK PELLRAIVD CGFEHPSEVQ HECIPQAILG MDVLCQAKSG MGKTAVFVLA TLQQLEPVTG QVSVLVMCHT RELAFQISKE Y ERFSKYMP ...String:
DYKDHDGDYK DHDIDYKDDD DKGSAAAMAE NDVDNELLDY EDDEVETAAG GDGAEAPAKK DVKGSYVSIH SSGFRDFLLK PELLRAIVD CGFEHPSEVQ HECIPQAILG MDVLCQAKSG MGKTAVFVLA TLQQLEPVTG QVSVLVMCHT RELAFQISKE Y ERFSKYMP NVKVAVFFGG LSIKKDEEVL KKNCPHIVVG TPGRILALAR NKSLNLKHIK HFILDECDKM LEQLDMRRDV QE IFRMTPH EKQVMMFSAT LSKEIRPVCR KFMQDPMEIF VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIF VKSVQR CIALAQLLVE QNFPAIAIHR GMPQEERLSR YQQFKDFQRR ILVATNLFGR GMDIERVNIA FNYDMPEDSD TYLH RVARA GRFGTKGLAI TFVSDENDAK ILNDVQDRFE VNISELPDEI DISSYIEQTR

UniProtKB: Spliceosome RNA helicase DDX39B

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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: 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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 99237
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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