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- EMDB-46983: Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1... -

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Entry
Database: EMDB / ID: EMD-46983
TitleCryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to the N-terminal motif of DDX39B(UAP56)
Map datastructure of a human TREX-2 complex
Sample
  • Complex: human TREX-2.1 complex and DDX39B
    • Protein or peptide: Leukocyte receptor cluster member 8
    • Protein or peptide: PCI domain-containing protein 2
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: Spliceosome RNA helicase DDX39B
KeywordsmRNA nuclear export / TREX / TREX-2 / LENG8 / UAP56 / DDX39B / RNA BINDING PROTEIN / RNA BINDING PROTEIN-Hydrolase complex
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 / integrator complex / mRNA 3'-end processing ...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 / integrator complex / 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) / Proteasome assembly / U4 snRNP / 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 / 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 / spliceosomal complex assembly / Presynaptic phase of homologous DNA pairing and strand exchange / U6 snRNA binding / mRNA export from nucleus / proteasome assembly / RHOBTB2 GTPase cycle / spleen development / 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 / Dectin-1 mediated noncanonical NF-kB signaling / spliceosomal complex / 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 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / 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 / 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 / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / protein transport
Similarity search - Function
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 ...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 / 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
26S proteasome complex subunit SEM1 / Spliceosome RNA helicase DDX39B / PCI domain-containing protein 2 / Leukocyte receptor cluster member 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 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) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46983.png

Downloads & links

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Map

FileDownload / File: emd_46983.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of a human TREX-2 complex
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: 0.14
Minimum - Maximum-0.4735997 - 0.84649897
Average (Standard dev.)-0.00027736233 (±0.014694992)
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_46983_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_46983_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-2.1 complex and DDX39B

EntireName: human TREX-2.1 complex and DDX39B
Components
  • Complex: human TREX-2.1 complex and DDX39B
    • Protein or peptide: Leukocyte receptor cluster member 8
    • Protein or peptide: PCI domain-containing protein 2
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: Spliceosome RNA helicase DDX39B

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Supramolecule #1: human TREX-2.1 complex and DDX39B

SupramoleculeName: human TREX-2.1 complex and DDX39B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Leukocyte receptor cluster member 8

MacromoleculeName: Leukocyte receptor cluster member 8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.909301 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSRSRKK MAALECEDPE RELKKQKRAA RFQHGHSRRL RLEPLVLQMS SLESSGADPD WQELQIVGTC PDITKHYLRL TCAPDPSTV RPVAVLKKSL CMVKCHWKEK QDYAFACEQM KSIRQDLTVQ GIRTEFTVEV YETHARIALE KGDHEEFNQC Q TQLKSLYA ...String:
GAMGSRSRKK MAALECEDPE RELKKQKRAA RFQHGHSRRL RLEPLVLQMS SLESSGADPD WQELQIVGTC PDITKHYLRL TCAPDPSTV RPVAVLKKSL CMVKCHWKEK QDYAFACEQM KSIRQDLTVQ GIRTEFTVEV YETHARIALE KGDHEEFNQC Q TQLKSLYA ENLPGNVGEF TAYRILYYIF TKNSGDITTE LAYLTRELKA DPCVAHALAL RTAWALGNYH RFFRLYCHAP CM SGYLVDK FADRERKVAL KAMIKTFRPA LPVSYLQAEL AFEGEAACRA FLEPLGLAYT GPDNSSIDCR LSLAQLSAF

UniProtKB: Leukocyte receptor cluster member 8

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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: 49.05625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQA KSGMGKTAVF VLATLQQLEP VTGQVSVLVM CHTRELAFQI SKEYERFSKY MPNVKVAVFF GGLSIKKDEE V LKKNCPHI ...String:
MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQA KSGMGKTAVF VLATLQQLEP VTGQVSVLVM CHTRELAFQI SKEYERFSKY MPNVKVAVFF GGLSIKKDEE V LKKNCPHI VVGTPGRILA LARNKSLNLK HIKHFILDEC DKMLEQLDMR RDVQEIFRMT PHEKQVMMFS ATLSKEIRPV CR KFMQDPM EIFVDDETKL TLHGLQQYYV KLKDNEKNRK LFDLLDVLEF NQVVIFVKSV QRCIALAQLL VEQNFPAIAI HRG MPQEER LSRYQQFKDF QRRILVATNL FGRGMDIERV NIAFNYDMPE DSDTYLHRVA RAGRFGTKGL AITFVSDEND AKIL NDVQD RFEVNISELP DEIDISSYIE QTR

UniProtKB: Spliceosome RNA helicase DDX39B

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.1 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 569284
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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