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- EMDB-54282: Cryo-EM structure of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex -

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Entry
Database: EMDB / ID: EMD-54282
TitleCryo-EM structure of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
Map dataCpmposite Map of the human SAC3D1-PCID2-SEM1-UAP56-RNA complex
Sample
  • Complex: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
    • Complex: Human SAC3D1-PCID2-SEM1 complex
      • Protein or peptide: SAC3 domain-containing protein 1
      • Protein or peptide: PCI domain-containing protein 2
      • Protein or peptide: 26S proteasome complex subunit SEM1
    • Complex: Human UAP56-RNA complex
      • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
      • Protein or peptide: Spliceosome RNA helicase DDX39B
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsmRNA export / GENE REGULATION
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 / spleen development / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / ATP-dependent activity, acting on RNA ...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 / spleen development / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / ATP-dependent activity, acting on RNA / mRNA 3'-end processing / ATP-dependent protein binding / integrator complex / U4 snRNP / RNA export from nucleus / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / proteasome regulatory particle, lid subcomplex / RNA Polymerase II Transcription Termination / positive regulation of B cell differentiation / poly(A)+ mRNA export from nucleus / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / cellular response to type I interferon / Cross-presentation of soluble exogenous antigens (endosomes) / negative regulation of gene expression, epigenetic / Somitogenesis / 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 / centrosome duplication / proteasome assembly / mRNA export from nucleus / spindle assembly / proteasome complex / spliceosomal complex / mRNA Splicing - Major Pathway / RNA splicing / regulation of proteasomal protein catabolic process / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Autodegradation of Cdh1 by Cdh1:APC/C / proteasomal protein catabolic process / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / mRNA splicing, via spliceosome / 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 / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / transcription elongation by RNA polymerase II / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / 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 / MAPK6/MAPK4 signaling / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / HDR through Homologous Recombination (HRR) / ABC-family protein mediated transport / spindle / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / SPOP-mediated proteasomal degradation of PD-L1(CD274) / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling
Similarity search - Function
Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / RNA helicase, DEAD-box type, Q motif / PCI/PINT associated module / DEAD-box RNA helicase Q motif profile. ...Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / RNA helicase, DEAD-box type, Q motif / PCI/PINT associated module / 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
SAC3 domain-containing protein 1 / 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: 2.62 Å
AuthorsHohmann U / Graf M / Plaschka C
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
H2020 Marie Curie Actions of the European Commission896416European Union
European Molecular Biology Organization (EMBO)ALTF_1175-2019European Union
CitationJournal: Nature / Year: 2026
Title: Molecular basis of polyadenylated RNA fate determination in the nucleus.
Authors: Andrii Bugai / Ulrich Hohmann / Ana Lorenzo / Max Graf / Laura Fin / Jérôme O Rouvière / Laszlo Tirian / Yuhui Dou / Marion Le Rest / Patrik Polák / Dennis Johnsen / Lis Jakobsen / Jens ...Authors: Andrii Bugai / Ulrich Hohmann / Ana Lorenzo / Max Graf / Laura Fin / Jérôme O Rouvière / Laszlo Tirian / Yuhui Dou / Marion Le Rest / Patrik Polák / Dennis Johnsen / Lis Jakobsen / Jens Skorstengaard Andersen / Julius Brennecke / Clemens Plaschka / Torben Heick Jensen /
Abstract: Eukaryotic genomes generate a plethora of polyadenylated (pA) RNAs, which are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA RNPs, including ...Eukaryotic genomes generate a plethora of polyadenylated (pA) RNAs, which are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA RNPs, including protein-coding RNPs, are exported to the cytoplasm, whereas transcripts within non-functional pA RNPs are degraded in the nucleus. How cells distinguish these opposing fates remains unknown. The DExD-box ATPase UAP56 (also known as DDX39B) is a central component of functional pA RNPs, and promotes their docking to the nuclear pore complex-anchored TREX-2, which triggers transcript release from UAP56 to facilitate export. Here we reveal that the poly(A) tail exosome targeting (PAXT) connection binds a TREX-2-like module, which releases pA RNAs from UAP56 for decay by the nuclear exosome. The core of this module consists of a LENG8-PCID2-SEM1 trimer, which we show is structurally and biochemically equivalent to the central GANP-PCID2-SEM1 trimer of TREX-2. Mutagenesis and transcriptomic data demonstrate that the nuclear fate of pA RNPs is governed by the contending actions of nucleoplasmic PAXT and nuclear pore complex-associated TREX-2, which interpret RNA-bound UAP56 as a signal for RNA decay or export, respectively. As RNA targets of PAXT are generally short and intron-poor, we propose an overall model for pA RNP fate determination whereby the distinct sub-nuclear localizations of PAXT and TREX-2 govern the degradation of short non-functional pA RNAs while allowing export of their longer and functional counterparts.
History
DepositionJul 6, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54282.png

Downloads & links

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Map

FileDownload / File: emd_54282.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCpmposite Map of the human SAC3D1-PCID2-SEM1-UAP56-RNA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 260 pix.
= 233.48 Å		0.9 Å/pix.
x 260 pix.
= 233.48 Å		0.9 Å/pix.
x 260 pix.
= 233.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.898 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3113013 - 2.0381994
Average (Standard dev.)0.0014486184 (±0.019987175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-2-2-2
Dimensions260260260
Spacing260260260
CellA=B=C: 233.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex

EntireName: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
Components
  • Complex: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
    • Complex: Human SAC3D1-PCID2-SEM1 complex
      • Protein or peptide: SAC3 domain-containing protein 1
      • Protein or peptide: PCI domain-containing protein 2
      • Protein or peptide: 26S proteasome complex subunit SEM1
    • Complex: Human UAP56-RNA complex
      • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
      • Protein or peptide: Spliceosome RNA helicase DDX39B
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex

SupramoleculeName: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human SAC3D1-PCID2-SEM1 complex

SupramoleculeName: Human SAC3D1-PCID2-SEM1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human UAP56-RNA complex

SupramoleculeName: Human UAP56-RNA complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.547529 KDa
SequenceString:
UUUUUUUUUU UUUUU

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Macromolecule #2: SAC3 domain-containing protein 1

MacromoleculeName: SAC3 domain-containing protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.615109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGRRAQTGS APPRPAAPHP RPASRAFPQH CRPRDAERPP SPRSPLMPGC ELPVGTCPDM CPAAERAQRE REHRLHRLEV VPGCRQDPP RADPQRAVKE YSRPAAGKPR PPPSQLRPPS VLLATVRYLA GEVAESADIA RAEVASFVAD RLRAVLLDLA L QGAGDAEA ...String:
MAGRRAQTGS APPRPAAPHP RPASRAFPQH CRPRDAERPP SPRSPLMPGC ELPVGTCPDM CPAAERAQRE REHRLHRLEV VPGCRQDPP RADPQRAVKE YSRPAAGKPR PPPSQLRPPS VLLATVRYLA GEVAESADIA RAEVASFVAD RLRAVLLDLA L QGAGDAEA AVVLEAALAT LLTVVARLGP DAARGPADPV LLQAQVQEGF GSLRRCYARG AGPHPRQPAF QGLFLLYNLG SV EALHEVL QLPAALRACP PLRKALAVDA AFREGNAARL FRLLQTLPYL PSCAVQCHVG HARREALARF ARAFSTPKGQ TLP LGFMVN LLALDGLREA RDLCQAHGLP LDGEERVVFL RGRYVEEGLP PASTCKVLVE SKLRGRTLEE VVMAEEEDEG TDRP GSPA

UniProtKB: SAC3 domain-containing protein 1

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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: 46.095883 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 #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: Spliceosome RNA helicase DDX39B

MacromoleculeName: Spliceosome RNA helicase DDX39B / type: protein_or_peptide / ID: 5 / 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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Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.7 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 129495
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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