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- PDB-9dlv: Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1... -

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Basic information

Entry
Database: PDB / ID: 9dlv
TitleCryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to DDX39B(UAP56)
Components
  • 26S proteasome complex subunit SEM1
  • Leukocyte receptor cluster member 8
  • PCI domain-containing protein 2
  • Spliceosome RNA helicase DDX39B
KeywordsRNA BINDING PROTEIN/Hydrolase / mRNA 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsClarke, B.P. / Xie, Y. / Ren, Y.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update
Revision 2.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Data updated
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte receptor cluster member 8
B: PCI domain-containing protein 2
C: 26S proteasome complex subunit SEM1
D: Spliceosome RNA helicase DDX39B


Theoretical massNumber of molelcules
Total (without water)139,8584
Polymers139,8584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Leukocyte receptor cluster member 8


Mass: 35909.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LENG8, KIAA1932 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PV6
#2: Protein PCI domain-containing protein 2 / CSN12-like protein


Mass: 46095.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCID2, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JVF3
#3: Protein 26S proteasome complex subunit SEM1 / 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot ...26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEM1, C7orf76, DSS1, SHFDG1, SHFM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P60896
#4: Protein Spliceosome RNA helicase DDX39B / 56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B- ...56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B-associated transcript 1 protein


Mass: 49567.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39B, BAT1, UAP56 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13838, RNA helicase
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human TREX-2 complex and DDX39B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 56.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 557019 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 89.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00247404
ELECTRON MICROSCOPYf_angle_d0.42429988
ELECTRON MICROSCOPYf_chiral_restr0.03811100
ELECTRON MICROSCOPYf_plane_restr0.00291275
ELECTRON MICROSCOPYf_dihedral_angle_d3.5656970

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