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- PDB-9t3x: cryo-EM structure of CPSF160-WDR33-ZC3H18 -

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Basic information

Entry
Database: PDB / ID: 9t3x
Titlecryo-EM structure of CPSF160-WDR33-ZC3H18
Components
  • Cleavage and polyadenylation specificity factor subunit 1
  • Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH domain-containing protein 18
  • pre-mRNA 3' end processing protein WDR33
KeywordsRNA BINDING PROTEIN / ZC3H18 / CPSF160 / WDR33 / Complex
Function / homology
Function and homology information


co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cap binding complex binding / RNA destabilization / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing ...co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cap binding complex binding / RNA destabilization / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / tRNA processing in the nucleus / DNA damage tolerance / RNA Polymerase II Transcription Termination / detection of maltose stimulus / maltose transport complex / carbohydrate transport / Processing of Capped Intron-Containing Pre-mRNA / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / fibrillar center / mRNA processing / outer membrane-bounded periplasmic space / spermatogenesis / protein-macromolecule adaptor activity / periplasmic space / nuclear speck / ribonucleoprotein complex / DNA damage response / enzyme binding / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus
Similarity search - Function
: / E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / Pre-mRNA 3' end processing protein Pfs2-like / Zinc finger, CCCH-type superfamily / zinc finger / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...: / E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / Pre-mRNA 3' end processing protein Pfs2-like / Zinc finger, CCCH-type superfamily / zinc finger / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / 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 / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Cleavage and polyadenylation specificity factor subunit 1 / Zinc finger CCCH domain-containing protein 18 / pre-mRNA 3' end processing protein WDR33
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsKuhn, C.C. / Chand, M.K. / Todesca, S. / Williams, K. / Keidel, A. / Garland, W. / Jensen, T.H. / Conti, E.
Funding support Germany, European Union, Denmark, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)740329European Union
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Direct coupling of the human nuclear exosome adaptors NEXT and PAXT with transcription termination and processing machineries.
Authors: Christopher C Kuhn / Mahesh K Chand / Sofia Todesca / Kathryn Williams / Achim Keidel / William Garland / Torben H Jensen / Elena Conti /
Abstract: In human cells, the Nuclear EXosome Targeting (NEXT) and Poly(A) tail eXosome Targeting (PAXT) adaptors direct the nuclear exosome to degrade prematurely terminated RNA Polymerase II (Pol II) ...In human cells, the Nuclear EXosome Targeting (NEXT) and Poly(A) tail eXosome Targeting (PAXT) adaptors direct the nuclear exosome to degrade prematurely terminated RNA Polymerase II (Pol II) transcripts, ensuring nuclear RNA quality control. How these adaptors interact with transcription termination machineries remains largely unclear. Here, we leveraged in silico structure predictions of protein complexes to identify and model previously unreported interactions of NEXT- and PAXT-associated components with two transcription termination and processing machineries, the Integrator and Cleavage and Polyadenylation (CPA) complexes. Our computational models were validated through complementary in vitro biochemical approaches and single-particle cryo-EM analyses. We show that the ZC3H18 protein uses two different domains to directly recognize the INTS9/11 endonuclease module of Integrator and the mammalian Polyadenylation Specificity Factor (mPSF), a core CPA component. In turn, ZC3H18 can directly bind the scaffolding subunits of NEXT and PAXT via mutually exclusive interactions. Furthermore, we provide evidence that accessory PAXT components can be directly integrated with the mPSF core, establishing configurations that are mutually exclusive with those of canonical CPA subunits. These findings reveal a versatile interaction network capable of forming alternative structural frameworks linking transcription termination with nuclear RNA quality control.
History
DepositionOct 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 1
B: pre-mRNA 3' end processing protein WDR33
C: Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH domain-containing protein 18


Theoretical massNumber of molelcules
Total (without water)265,1853
Polymers265,1853
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 Cleavage and polyadenylation specificity factor subunit 1


Mass: 161074.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q10570
#2: Protein pre-mRNA 3' end processing protein WDR33 / WD repeat-containing protein 33 / WD repeat-containing protein of 146 kDa


Mass: 53164.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal TwinStrep tag, C-terminal FLAG-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: WDR33, WDC146 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9C0J8
#3: Protein Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH domain-containing protein 18 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nuclear protein NHN1


Mass: 50946.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, ...Details: sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, ZC3H18, NHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q86VM9
Has protein modificationN

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1CPSF160-WDR33 core complex with ZC3H18COMPLEXZC3H18 uses two anchor points to interact with CPSF160all0RECOMBINANT
2CPSF160-WDR33 core complexCOMPLEX#1-#21RECOMBINANT
3ZC3H18COMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.5 / Details: 20mM HEPES pH 7.5, 150mM NaCl, 5mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium clorideNaCl1
35 mMmagnesium clorideMgCl21
40.04 %n-octyl-beta-d-glucoside14H28O61
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 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 defocus max: 2200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 61.65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selectioncryoSPARC implementation
2PHENIX1.21.2_5419model refinement
3SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1512004 / Symmetry type: POINT
RefinementHighest resolution: 2.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312789
ELECTRON MICROSCOPYf_angle_d0.60317367
ELECTRON MICROSCOPYf_dihedral_angle_d12.9944641
ELECTRON MICROSCOPYf_chiral_restr0.0461951
ELECTRON MICROSCOPYf_plane_restr0.0042217

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