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

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Basic information

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 / negative regulation of transcription initiation by RNA polymerase II / transcription export complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / heterochromatin organization / 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) ...negative regulation of lymphoid progenitor cell differentiation / negative regulation of transcription initiation by RNA polymerase II / transcription export complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / heterochromatin organization / 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 protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / proteasome regulatory particle, lid subcomplex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / U4 snRNP / Regulation of ornithine decarboxylase (ODC) / RNA Polymerase II Transcription Termination / Proteasome assembly / 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 / Cross-presentation of soluble exogenous antigens (endosomes) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of B cell differentiation / Somitogenesis / poly(A)+ mRNA export from nucleus / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression, epigenetic / histone acetyltransferase activity / spliceosomal complex assembly / Presynaptic phase of homologous DNA pairing and strand exchange / somatic hypermutation of immunoglobulin genes / proteasome assembly / U6 snRNA binding / mRNA export from nucleus / RHOBTB2 GTPase cycle / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / spleen development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mRNA Splicing - Major Pathway / 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 / 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 / transcription elongation by RNA polymerase II / 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 / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / double-strand break repair via homologous recombination / Degradation of GLI2 by the proteasome
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: To Be Published
Title: Mechanisms of mRNP remodeling by human TREX-2 complex
Authors: Clarke BP / Xie Y / Ren Y
History
DepositionSep 11, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 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)
Density Histograms

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

Projections

Slices (1/2)
Density Histograms

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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