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- EMDB-46982: Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56) -

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Entry
Database: EMDB / ID: EMD-46982
TitleCryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56)
Map datastructure of human TREX-2 complex bound to DDX39B(UAP56)
Sample
  • Complex: human TREX-2 complex and DDX39B
    • 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: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsmRNA nuclear export / TREX / TREX-2 / UAP56 / DDX39B / RNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / transcription export complex / U6 snRNP / transcription export complex 2 / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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 / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / histone H3 acetyltransferase activity / integrator complex / nucleosome organization / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / ATP-dependent protein binding / proteasome regulatory particle, lid subcomplex / U4 snRNA binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / Regulation of ornithine decarboxylase (ODC) / U4 snRNP / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / 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) / positive regulation of B cell differentiation / Resolution of D-loop Structures through Holliday Junction Intermediates / Somitogenesis / poly(A)+ mRNA export from nucleus / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression, epigenetic / spliceosomal complex assembly / Presynaptic phase of homologous DNA pairing and strand exchange / U6 snRNA binding / mRNA export from nucleus / proteasome assembly / RHOBTB2 GTPase cycle / histone acetyltransferase activity / somatic hypermutation of immunoglobulin genes / histone acetyltransferase / spleen development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mRNA Splicing - Major Pathway / RNA splicing / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / spliceosomal complex / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / transcription elongation by RNA polymerase II / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Regulation of RUNX3 expression and activity / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / double-strand break repair via homologous recombination / mRNA splicing, via spliceosome / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / HDR through Homologous Recombination (HRR) / ABC-family proteins mediated transport / 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 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif 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: 2.79 Å
AuthorsClarke 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: Nat Commun / Year: 2025
Title: Structural mechanism of DDX39B regulation by human TREX-2 and a related complex in mRNP remodeling.
Authors: Bradley P Clarke / Shengyan Gao / Menghan Mei / Dongqi Xie / Alexia E Angelos / Ashley Vazhavilla / Pate S Hill / Tolga Cagatay / Kimberly Batten / Jerry W Shay / Yihu Xie / Beatriz M A Fontoura / Yi Ren /
Abstract: Nuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a ...Nuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a multifunctional regulator of nuclear mRNPs. How DDX39B mediates mRNP assembly and export in a controlled manner remains elusive. Here, we identify a novel complex TREX-2.1 localized in the nucleus that facilitates the release of DDX39B from the mRNP. TREX-2.1 is composed of three subunits, LENG8, PCID2, and DSS1, and shares the latter two subunits with the nuclear pore complex-associated TREX-2 complex. Cryo-EM structures of TREX-2.1/DDX39B and TREX-2/DDX39B identify a conserved trigger loop in the LENG8 and GANP subunit of the respective TREX-2.1 and TREX-2 complex that is critical for DDX39B regulation. RNA sequencing from LENG8 knockdown cells shows that LENG8 influences the nucleocytoplasmic ratio of a subset of mRNAs with high GC content. Together, our findings lead to a mechanistic understanding of the functional cycle of DDX39B and its regulation by TREX-2 and TREX-2.1 in mRNP processing.
History
DepositionSep 11, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46982.png

Downloads & links

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Map

FileDownload / File: emd_46982.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of human TREX-2 complex bound to DDX39B(UAP56)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 236.16 Å		0.82 Å/pix.
x 288 pix.
= 236.16 Å		0.82 Å/pix.
x 288 pix.
= 236.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.5032652 - 0.8476708
Average (Standard dev.)-0.00030517404 (±0.019582795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 236.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_46982_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46982_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human TREX-2 complex and DDX39B

EntireName: human TREX-2 complex and DDX39B
Components
  • Complex: human TREX-2 complex and DDX39B
    • 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: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: human TREX-2 complex and DDX39B

SupramoleculeName: human TREX-2 complex and DDX39B / type: complex / 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 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.607586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSKEAKK ETGFVESAES DHMAIPGGNQ SVLAPSRIPG VNKEEETESR EKKEDSLRGT PARQSNRSES TDSLGGLSPS EVTAIQCKN IPDYLNDRTI LENHFGKIAK VQRIFTRRSK KLAVVHFFDH ASAALARKKG KSLHKDMAIF WHRKKISPNK K PFSLKEKK ...String:
GAMGSKEAKK ETGFVESAES DHMAIPGGNQ SVLAPSRIPG VNKEEETESR EKKEDSLRGT PARQSNRSES TDSLGGLSPS EVTAIQCKN IPDYLNDRTI LENHFGKIAK VQRIFTRRSK KLAVVHFFDH ASAALARKKG KSLHKDMAIF WHRKKISPNK K PFSLKEKK PGDGEVSPST EDAPFQHSPL GKAAGRTGAS SLLNKSSPVK KPSLLKAHQF EGDSFDSASE GSEGLGPCVL SL STLIGTV AETSKEKYRL LDQRDRIMRQ ARVKRTDLDK ARTFVGTCLD MCPEKERYMR ETRSQLSVFE VVPGTDQVDH AAA VKEYSR SSADQEEPLP HELRPLPVLS RTMDYLVTQI MDQKEGSLRD WYDFVWNRTR GIRKDITQQH LCDPLTVSLI EKCT RFHIH CAHFMCEEPM SSFDAKINNE NMTKCLQSLK EMYQDLRNKG VFCASEAEFQ GYNVLLSLNK GDILREVQQF HPAVR NSSE VKFAVQAFAA LNSNNFVRFF KLVQSASYLN ACLLHCYFSQ IRKDALRALN FAYTVSTQRS TIFPLDGVVR MLLFRD CEE ATDFLTCHGL TVSDGCVELN RSAFLEPEGL SKTRKSVFIT RKLTVSVGEI VNGGPLPPVP RHTPVCSFNS QNKYIGE SL AAELPV

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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.095883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHITINQYL QQVYEAIDSR DGASCAELVS FKHPHVANPR LQMASPEEKC QQVLEPPYDE MFAAHLRCTY AVGNHDFIEA YKCQTVIVQ SFLRAFQAHK EENWALPVMY AVALDLRVFA NNADQQLVKK GKSKVGDMLE KAAELLMSCF RVCASDTRAG I EDSKKWGM ...String:
MAHITINQYL QQVYEAIDSR DGASCAELVS FKHPHVANPR LQMASPEEKC QQVLEPPYDE MFAAHLRCTY AVGNHDFIEA YKCQTVIVQ SFLRAFQAHK EENWALPVMY AVALDLRVFA NNADQQLVKK GKSKVGDMLE KAAELLMSCF RVCASDTRAG I EDSKKWGM LFLVNQLFKI YFKINKLHLC KPLIRAIDSS NLKDDYSTAQ RVTYKYYVGR KAMFDSDFKQ AEEYLSFAFE HC HRSSQKN KRMILIYLLP VKMLLGHMPT VELLKKYHLM QFAEVTRAVS EGNLLLLHEA LAKHEAFFIR CGIFLILEKL KII TYRNLF KKVYLLLKTH QLSLDAFLVA LKFMQVEDVD IDEVQCILAN LIYMGHVKGY ISHQHQKLVV SKQNPFPPLS TVC

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: Escherichia coli (E. coli)
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 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.567883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSMAEND VDNELLDYED DEVETAAGGD GAEAPAKKDV KGSYVSIHSS GFRDFLLKPE LLRAIVDCGF EHPSEVQHEC IPQAILGMD VLCQAKSGMG KTAVFVLATL QQL(A1AMM)PVTGQV SVLVMCHTRE LAFQISKEYE RFSKYMPNVK VAVFF GGLS ...String:
GAMGSMAEND VDNELLDYED DEVETAAGGD GAEAPAKKDV KGSYVSIHSS GFRDFLLKPE LLRAIVDCGF EHPSEVQHEC IPQAILGMD VLCQAKSGMG KTAVFVLATL QQL(A1AMM)PVTGQV SVLVMCHTRE LAFQISKEYE RFSKYMPNVK VAVFF GGLS IKKDEEVLKK NCPHIVVGTP GRILALARNK SLNLKHIKHF ILDECDKMLE QLDMRRDVQE IFRMTPHEKQ VMMFSA TLS KEIRPVCRKF MQDPMEIFVD DETKLTLHGL QQYYVKLKDN EKNRKLFDLL DVLEFNQVVI FVKSVQRCIA LAQLLVE QN FPAIAIHRGM PQEERLSRYQ QFKDFQRRIL VATNLFGRGM DIERVNIAFN YDMPEDSDTY LHRVARAGRF GTKGLAIT F VSDENDAKIL NDVQDRFEVN ISELPDEIDI SSYIEQTR

UniProtKB: Spliceosome RNA helicase DDX39B

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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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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 720007
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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