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- EMDB-56931: Cryo-EM structure of the human LENG8-PCID2-SEM1 complex -

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Entry
Database: EMDB / ID: EMD-56931
TitleCryo-EM structure of the human LENG8-PCID2-SEM1 complex
Map dataCryo-EM map of the human LENG8-PCID2-SEM1 complex (Map D)
Sample
  • Complex: Human LENG8-PCID2-SEM1 complex
    • Complex: Human LENG8-PCID2-SEM1 complex
      • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Leukocyte receptor cluster member 8
      • Protein or peptide: PCI domain-containing protein 2
      • Protein or peptide: 26S proteasome complex subunit SEM1
KeywordsmRNA export / GENE REGULATION
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / 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) / integrator complex / proteasome regulatory particle, lid subcomplex / positive regulation of B cell differentiation ...negative regulation of lymphoid progenitor cell differentiation / 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) / integrator complex / proteasome regulatory particle, lid subcomplex / 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 / detection of maltose stimulus / Impaired BRCA2 binding to RAD51 / carbohydrate transport / carbohydrate transmembrane transporter activity / Presynaptic phase of homologous DNA pairing and strand exchange / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / proteasome assembly / mRNA export from nucleus / proteasome complex / ATP-binding cassette (ABC) transporter complex / regulation of proteasomal protein catabolic process / cell chemotaxis / 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 / 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 / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Regulation of RAS by GAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / synaptic vesicle
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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / 26S proteasome complex subunit SEM1 / PCI domain-containing protein 2 / Leukocyte receptor cluster member 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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
DepositionFeb 25, 2026-
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_56931.png

Downloads & links

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Map

FileDownload / File: emd_56931.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the human LENG8-PCID2-SEM1 complex (Map D)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 224.768 Å		0.88 Å/pix.
x 256 pix.
= 224.768 Å		0.88 Å/pix.
x 256 pix.
= 224.768 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.6445849 - 0.9991642
Average (Standard dev.)0.0001435026 (±0.022292024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 224.768 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of the human LENG8-PCID2-SEM1 complex (Map D), half map A

Fileemd_56931_half_map_1.map
AnnotationCryo-EM map of the human LENG8-PCID2-SEM1 complex (Map D), half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of the human LENG8-PCID2-SEM1 complex (Map D), half map B

Fileemd_56931_half_map_2.map
AnnotationCryo-EM map of the human LENG8-PCID2-SEM1 complex (Map D), half 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 LENG8-PCID2-SEM1 complex

EntireName: Human LENG8-PCID2-SEM1 complex
Components
  • Complex: Human LENG8-PCID2-SEM1 complex
    • Complex: Human LENG8-PCID2-SEM1 complex
      • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Leukocyte receptor cluster member 8
      • Protein or peptide: PCI domain-containing protein 2
      • Protein or peptide: 26S proteasome complex subunit SEM1

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Supramolecule #1: Human LENG8-PCID2-SEM1 complex

SupramoleculeName: Human LENG8-PCID2-SEM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human LENG8-PCID2-SEM1 complex

SupramoleculeName: Human LENG8-PCID2-SEM1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Leukocyte recept...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,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: 76.698383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KIEEGKLVIW INGDKGYNGL AEVGKKFEKD TGIKVTVEHP DKLEEKFPQV AATGDGPDII FWAHDRFGGY AQSGLLAEIT PDKAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAKGKSALMF NLQEPYFTWP L IAADGGYA ...String:
KIEEGKLVIW INGDKGYNGL AEVGKKFEKD TGIKVTVEHP DKLEEKFPQV AATGDGPDII FWAHDRFGGY AQSGLLAEIT PDKAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAKGKSALMF NLQEPYFTWP L IAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLVDL IKNKHMNADT DYSIAEAAFN KGETAMTING PWAWSNIDTS KV NYGVTVL PTFKGQPSKP FVGVLSAGIN AASPNKELAK EFLENYLLTD EGLEAVNKDK PLGAVALKSY EEELAKDPRI AAT MENAQK GEIMPNIPQM SAFWYAVRTA VINAASGRQT VDEALKDAQT SSGLEVLFQG PSRKKMAALE CEDPERELKK QKRA ARFQH GHSRRLRLEP LVLQMSSLES SGADPDWQEL QIVGTCPDIT KHYLRLTCAP DPSTVRPVAV LKKSLCMVKC HWKEK QDYA FACEQMKSIR QDLTVQGIRT EFTVEVYETH ARIALEKGDH EEFNQCQTQL KSLYAENLPG NVGEFTAYRI LYYIFT KNS GDITTELAYL TRELKADPCV AHALALRTAW ALGNYHRFFR LYCHAPCMSG YLVDKFADRE RKVALKAMIK TFRPALP VS YLQAELAFEG EAACRAFLEP LGLAYTGPDN SSIDCRLSLA QLSAF

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, 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: 51.713254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GKPIPNPLLG LDSTGSGKPI PNPLLGLDST GSGKPIPNPL LGLDSTSSGL EVLFQGPMAH ITINQYLQQV YEAIDSRDGA SCAELVSFK HPHVANPRLQ MASPEEKCQQ VLEPPYDEMF AAHLRCTYAV GNHDFIEAYK CQTVIVQSFL RAFQAHKEEN W ALPVMYAV ...String:
GKPIPNPLLG LDSTGSGKPI PNPLLGLDST GSGKPIPNPL LGLDSTSSGL EVLFQGPMAH ITINQYLQQV YEAIDSRDGA SCAELVSFK HPHVANPRLQ MASPEEKCQQ VLEPPYDEMF AAHLRCTYAV GNHDFIEAYK CQTVIVQSFL RAFQAHKEEN W ALPVMYAV ALDLRVFANN ADQQLVKKGK SKVGDMLEKA AELLMSCFRV CASDTRAGIE DSKKWGMLFL VNQLFKIYFK IN KLHLCKP LIRAIDSSNL KDDYSTAQRV TYKYYVGRKA MFDSDFKQAE EYLSFAFEHC HRSSQKNKRM ILIYLLPVKM LLG HMPTVE LLKKYHLMQF AEVTRAVSEG NLLLLHEALA KHEAFFIRCG IFLILEKLKI ITYRNLFKKV YLLLKTHQLS LDAF LVALK FMQVEDVDID EVQCILANLI YMGHVKGYIS HQHQKLVVSK QNPFPPLSTV C

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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30462
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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