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- EMDB-55619: Cryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56 -

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Entry
Database: EMDB / ID: EMD-55619
TitleCryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56
Map data
Sample
  • Complex: Cryo-EM structure of the human GANP-PID2-DSS1 complex bound to UAP56
    • Protein or peptide: Spliceosome RNA helicase 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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsRNA metabolism / RNA export / NUCLEAR PROTEIN
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 / nuclear pore nuclear basket / histone H3 acetyltransferase activity / nucleosome organization / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) ...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 / nuclear pore nuclear basket / histone H3 acetyltransferase activity / nucleosome organization / 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 / 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 / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / histone acetyltransferase activity / 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 / spliceosomal complex assembly / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / U6 snRNA binding / RHOBTB2 GTPase cycle / somatic hypermutation of immunoglobulin genes / histone acetyltransferase / proteasome assembly / mRNA export from nucleus / spleen development / mRNA Splicing - Major Pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 / 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 / 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 / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin
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 / 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 / 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: 3.0 Å
AuthorsAbbas DK / Bonneau F / Basquin J / Conti E / Schussler S / Wilkinson ME
Funding supportEuropean Union, Germany, Denmark, 3 items
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, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55619.png

Downloads & links

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Map

FileDownload / File: emd_55619.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 245.146 Å		0.85 Å/pix.
x 288 pix.
= 245.146 Å		0.85 Å/pix.
x 288 pix.
= 245.146 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.07247784 - 0.24082918
Average (Standard dev.)0.0017377847 (±0.007973642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 245.1456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55619_msk_1.map
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Half map: #2

Fileemd_55619_half_map_1.map
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Half map: #1

Fileemd_55619_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the human GANP-PID2-DSS1 complex bound to UAP56

EntireName: Cryo-EM structure of the human GANP-PID2-DSS1 complex bound to UAP56
Components
  • Complex: Cryo-EM structure of the human GANP-PID2-DSS1 complex bound to UAP56
    • Protein or peptide: Spliceosome RNA helicase 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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of the human GANP-PID2-DSS1 complex bound to UAP56

SupramoleculeName: Cryo-EM structure of the human GANP-PID2-DSS1 complex bound to UAP56
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spliceosome RNA helicase DDX39B

MacromoleculeName: Spliceosome RNA helicase DDX39B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.412582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAENDV DNELLDYEDD EVETAAGGDG AEAPAKKDVK GSYVSIHSSG FRDFLLKPEL LRAIVDCGFE HPSEVQHECI PQAILGMDV LCQAKSGMGK TAVFVLATLQ QLEPVTGQVS VLVMCHTREL AFQISKEYER FSKYMPNVKV AVFFGGLSIK K DEEVLKKN ...String:
GPDSMAENDV DNELLDYEDD EVETAAGGDG AEAPAKKDVK GSYVSIHSSG FRDFLLKPEL LRAIVDCGFE HPSEVQHECI PQAILGMDV LCQAKSGMGK TAVFVLATLQ QLEPVTGQVS VLVMCHTREL AFQISKEYER FSKYMPNVKV AVFFGGLSIK K DEEVLKKN CPHIVVGTPG RILALARNKS LNLKHIKHFI LDECDKMLEQ LDMRRDVQEI FRMTPHEKQV MMFSATLSKE IR PVCRKFM QDPMEIFVDD ETKLTLHGLQ QYYVKLKDNE KNRKLFDLLD VLEFNQVVIF VKSVQRCIAL AQLLVEQNFP AIA IHRGMP QEERLSRYQQ FKDFQRRILV ATNLFGRGMD IERVNIAFNY DMPEDSDTYL HRVARAGRFG TKGLAITFVS DEND AKILN DVQDRFEVNI SELPDEIDIS SYIEQTR

UniProtKB: Spliceosome RNA helicase DDX39B

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Macromolecule #2: Germinal-center associated nuclear protein

MacromoleculeName: Germinal-center associated nuclear protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.363887 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDMTVAETS KEKYRLLDQR DRIMRQARVK RTDLDKARTF VGTCLDMCPE KERYMRETRS QLSVFEVVPG TDQVDHAAAV KEYSRSSAD QEEPLPHELR PLPVLSRTMD YLVTQIMDQK EGSLRDWYDF VWNRTRGIRK DITQQHLCDP LTVSLIEKCT R FHIHCAHF ...String:
GPDMTVAETS KEKYRLLDQR DRIMRQARVK RTDLDKARTF VGTCLDMCPE KERYMRETRS QLSVFEVVPG TDQVDHAAAV KEYSRSSAD QEEPLPHELR PLPVLSRTMD YLVTQIMDQK EGSLRDWYDF VWNRTRGIRK DITQQHLCDP LTVSLIEKCT R FHIHCAHF MCEEPMSSFD AKINNENMTK CLQSLKEMYQ DLRNKGVFCA SEAEFQGYNV LLSLNKGDIL REVQQFHPAV RN SSEVKFA VQAFAALNSN NFVRFFKLVQ SASYLNACLL HCYFSQIRKD ALRALNFAYT VSTQRSTIFP LDGVVRMLLF RDC EEATDF LTCHGLTVSD GCVELNRSAF LEPEGLSKTR KSVFITRKLT VSVGEIVNGG PLPPVPRHTP VCSFNSQNKY IGES LAAEL

UniProtKB: Germinal-center associated nuclear protein

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Macromolecule #3: PCI domain-containing protein 2

MacromoleculeName: PCI domain-containing protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.458289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSMAHITI NQYLQQVYEA IDSRDGASCA ELVSFKHPHV ANPRLQMASP EEKCQQVLEP PYDEMFAAHL RCTYAVGNHD FIEAYKCQT VIVQSFLRAF QAHKEENWAL PVMYAVALDL RVFANNADQQ LVKKGKSKVG DMLEKAAELL MSCFRVCASD T RAGIEDSK ...String:
MGSSMAHITI NQYLQQVYEA IDSRDGASCA ELVSFKHPHV ANPRLQMASP EEKCQQVLEP PYDEMFAAHL RCTYAVGNHD FIEAYKCQT VIVQSFLRAF QAHKEENWAL PVMYAVALDL RVFANNADQQ LVKKGKSKVG DMLEKAAELL MSCFRVCASD T RAGIEDSK KWGMLFLVNQ LFKIYFKINK LHLCKPLIRA IDSSNLKDDY STAQRVTYKY YVGRKAMFDS DFKQAEEYLS FA FEHCHRS SQKNKRMILI YLLPVKMLLG HMPTVELLKK YHLMQFAEVT RAVSEGNLLL LHEALAKHEA FFIRCGIFLI LEK LKIITY RNLFKKVYLL LKTHQLSLDA FLVALKFMQV EDVDIDEVQC ILANLIYMGH VKGYISHQHQ KLVVSKQNPF PPLS TVC

UniProtKB: PCI domain-containing protein 2

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Macromolecule #4: 26S proteasome complex subunit SEM1

MacromoleculeName: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 4 / 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 #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: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 28229 / Average electron dose: 61.8 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: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 661235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot (ver. 0.9.8.95)
Output model

PDB-9t6n:
Cryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56

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