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- PDB-9t6l: Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to ... -

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Basic information

Entry
Database: PDB / ID: 9t6l
TitleCryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B
Components
  • 26S proteasome complex subunit SEM1
  • Leukocyte receptor cluster member 8,Ribosomal RNA processing protein 1 homolog B
  • PCI domain-containing protein 2
  • Spliceosome RNA helicase DDX39B
KeywordsNUCLEAR PROTEIN / RNA metabolism / RNA decay / splicing quality control
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / granular component / transcription export complex / U6 snRNP / negative regulation of GTPase activity / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) ...negative regulation of lymphoid progenitor cell differentiation / granular component / transcription export complex / U6 snRNP / negative regulation of GTPase activity / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / ATP-dependent activity, acting on RNA / mRNA 3'-end processing / integrator complex / ATP-dependent protein binding / host-mediated activation of viral transcription / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNA binding / proteasome regulatory particle, lid subcomplex / RNA Polymerase II Transcription Termination / U4 snRNP / positive regulation of B cell differentiation / Regulation of ornithine decarboxylase (ODC) / poly(A)+ mRNA export from nucleus / Proteasome assembly / preribosome, small subunit precursor / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / negative regulation of gene expression, epigenetic / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of RNA splicing / spliceosomal complex assembly / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / U6 snRNA binding / RHOBTB2 GTPase cycle / proteasome assembly / mRNA export from nucleus / spleen development / heterochromatin / mRNA Splicing - Major Pathway / RNA splicing / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / spliceosomal complex / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / transcription elongation by RNA polymerase II / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / euchromatin / mRNA splicing, via spliceosome / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / cellular response to virus / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / Degradation of CDH1 / double-strand break repair via homologous recombination / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / ABC-family protein mediated transport / HDR through Homologous Recombination (HRR) / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / mRNA processing / Regulation of expression of SLITs and ROBOs
Similarity search - Function
Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module ...Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / PCI domain / Proteasome component (PCI) domain / PCI domain 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 / Ribosomal RNA processing protein 1 homolog B / 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: 2.9 Å
AuthorsAbbas, D.K. / Bonneau, F. / Basquin, J. / Conti, E. / Schussler, S. / Wilkinson, M.E.
Funding supportEuropean Union, Germany, Denmark, 3items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
German Research Foundation (DFG) Germany
Novo Nordisk Foundation Denmark
CitationJournal: Genes Dev / Year: 2026
Title: Evolutionarily conserved spliceosome-exosome pathway in nuclear mRNA surveillance.
Authors: Daniel K Abbas / Fabien Bonneau / Max E Wilkinson / Steffen Schüssler / Jérôme Basquin / Elena Conti /
Abstract: Intron-containing mRNAs are cotranscriptionally spliced and assembled into messenger ribonucleoprotein (mRNP) particles, a process monitored by surveillance pathways. Here, we combined biochemical ...Intron-containing mRNAs are cotranscriptionally spliced and assembled into messenger ribonucleoprotein (mRNP) particles, a process monitored by surveillance pathways. Here, we combined biochemical and structural approaches to elucidate the mechanisms by which mRNPs are sorted between two opposing fates: nuclear degradation and cytoplasmic export. While the human GANP-PCID2 complex is known to connect mRNPs to nuclear export, our data indicate that the LENG8-PCID2 complex operates as an mRNP decay connector, coupling nuclear mRNPs to the RNA-degrading exosome via the PAXT adaptor complex. Both recognize the mRNP component UAP56, but LENG8-PCID2 uniquely associates with early splicing factors through a direct interaction with U1A and RRP1B. Similarly, the Thp3-Csn12 ortholog in budding yeast couples the early splicing factors Mud2-Bbp with the nuclear exosome. The spliceosome-exosome mRNP decay pathway we uncovered reveals molecular principles that remain strikingly conserved across evolution, despite the fundamental differences in splicing and decay between humans and budding yeast.
History
DepositionNov 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spliceosome RNA helicase DDX39B
C: Leukocyte receptor cluster member 8,Ribosomal RNA processing protein 1 homolog B
D: PCI domain-containing protein 2
E: 26S proteasome complex subunit SEM1


Theoretical massNumber of molelcules
Total (without water)135,0094
Polymers135,0094
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 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: 49412.582 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
#2: Protein Leukocyte receptor cluster member 8,Ribosomal RNA processing protein 1 homolog B / RRP1-like protein B


Mass: 30940.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chains C and F are part of the same fusion protein (LENG8(550-800)-GS-RRP1B(742-758). Chain C is LENG8(550-800)., Chains C and F are part of the same fusion protein (LENG8(550-800)-GS- ...Details: Chains C and F are part of the same fusion protein (LENG8(550-800)-GS-RRP1B(742-758). Chain C is LENG8(550-800)., Chains C and F are part of the same fusion protein (LENG8(550-800)-GS-RRP1B(742-758). Chain F is RRP1B(742-758).,Chains C and F are part of the same fusion protein (LENG8(550-800)-GS-RRP1B(742-758). Chain C is LENG8(550-800)., Chains C and F are part of the same fusion protein (LENG8(550-800)-GS-RRP1B(742-758). Chain F is RRP1B(742-758).
Source: (gene. exp.) Homo sapiens (human) / Gene: LENG8, KIAA1932, RRP1B, KIAA0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PV6, UniProt: Q14684
#3: Protein PCI domain-containing protein 2 / CSN12-like protein


Mass: 46371.211 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
#4: 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
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: Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B
Type: COMPLEX / Entity ID: #1, #3-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 61.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 28229
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.0particle selection
2Topazparticle selection
5cryoSPARC4.7.0CTF correctionPatch CTF Estimation
8Coot0.9.8.95model fitting
9UCSF ChimeraX1.1model fitting
14cryoSPARC4.7.03D reconstruction
15PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 892731 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.9 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025526
ELECTRON MICROSCOPYf_angle_d0.4627467
ELECTRON MICROSCOPYf_dihedral_angle_d3.471727
ELECTRON MICROSCOPYf_chiral_restr0.036822
ELECTRON MICROSCOPYf_plane_restr0.003951

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