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- EMDB-55520: cryo-EM map of the human mPSF with FIP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-55520
Titlecryo-EM map of the human mPSF with FIP1
Map data
Sample
  • Complex: the human mPSF complex with FIP1 coordinated by CPSF30 at the CPSF160 subunit
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 1
    • Protein or peptide: pre-mRNA 3' end processing protein WDR33
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 4
    • Protein or peptide: Pre-mRNA 3'-end-processing factor FIP1
KeywordsmPSF / FIP1 / CPSF160 / WDR33 / Complex / zinc finger / RNA BINDING PROTEIN
Function / homology
Function and homology information


co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / Inhibition of Host mRNA Processing and RNA Silencing / 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 / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / Inhibition of Host mRNA Processing and RNA Silencing / 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 / Processing of Capped Intron-Containing Pre-mRNA / fibrillar center / mRNA processing / sequence-specific double-stranded DNA binding / spermatogenesis / intracellular membrane-bounded organelle / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Pre-mRNA polyadenylation factor Fip1 domain / : / Fip1 motif / Zinc-finger CCCH domain / Zinc-finger containing family / CPSF complex subunit CPSF4-like / Pre-mRNA 3' end processing protein Pfs2-like / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger ...Pre-mRNA polyadenylation factor Fip1 domain / : / Fip1 motif / Zinc-finger CCCH domain / Zinc-finger containing family / CPSF complex subunit CPSF4-like / Pre-mRNA 3' end processing protein Pfs2-like / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / 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 / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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
Cleavage and polyadenylation specificity factor subunit 4 / Cleavage and polyadenylation specificity factor subunit 1 / Pre-mRNA 3'-end-processing factor FIP1 / pre-mRNA 3' end processing protein WDR33
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsKuhn CC / Chand MK / Todesca S / Williams K / Keidel A / Garland W / Jensen TH / Conti E
Funding support Germany, European Union, Denmark, 5 items
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: RNA / Year: 2024
Title: Molecular basis of human poly(A) polymerase recruitment by mPSF.
Authors: Sofia Todesca / Felix Sandmeir / Achim Keidel / Elena Conti /
Abstract: 3' end processing of most eukaryotic precursor-mRNAs (pre-mRNAs) is a crucial cotranscriptional process that generally involves the cleavage and polyadenylation of the precursor transcripts. Within ...3' end processing of most eukaryotic precursor-mRNAs (pre-mRNAs) is a crucial cotranscriptional process that generally involves the cleavage and polyadenylation of the precursor transcripts. Within the human 3' end processing machinery, the four-subunit mammalian polyadenylation specificity factor (mPSF) recognizes the polyadenylation signal (PAS) in the pre-mRNA and recruits the poly(A) polymerase α (PAPOA) to it. To shed light on the molecular mechanisms of PAPOA recruitment to mPSF, we used a combination of cryogenic-electron microscopy (cryo-EM) single-particle analysis, computational structure prediction, and in vitro biochemistry to reveal an intricate interaction network. A short linear motif in the mPSF subunit FIP1 interacts with the structured core of human PAPOA, with a binding mode that is evolutionarily conserved from yeast to human. In higher eukaryotes, however, PAPOA contains a conserved C-terminal motif that can interact intramolecularly with the same residues of the PAPOA structured core used to bind FIP1. Interestingly, using biochemical assay and cryo-EM structural analysis, we found that the PAPOA C-terminal motif can also directly interact with mPSF at the subunit CPSF160. These results show that PAPOA recruitment to mPSF is mediated by two distinct intermolecular connections and further suggest the presence of mutually exclusive interactions in the regulation of 3' end processing.
History
DepositionOct 30, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55520.png

Downloads & links

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Map

FileDownload / File: emd_55520.map.gz / Format: CCP4 / Size: 85.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 282 pix.
= 240.038 Å		0.85 Å/pix.
x 282 pix.
= 240.038 Å		0.85 Å/pix.
x 282 pix.
= 240.038 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.315
Minimum - Maximum-0.3970081 - 1.4421694
Average (Standard dev.)0.010390947 (±0.0681558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282282282
Spacing282282282
CellA=B=C: 240.03839 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55520_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55520_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the human mPSF complex with FIP1 coordinated by CPSF30 at the CPS...

EntireName: the human mPSF complex with FIP1 coordinated by CPSF30 at the CPSF160 subunit
Components
  • Complex: the human mPSF complex with FIP1 coordinated by CPSF30 at the CPSF160 subunit
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 1
    • Protein or peptide: pre-mRNA 3' end processing protein WDR33
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 4
    • Protein or peptide: Pre-mRNA 3'-end-processing factor FIP1

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Supramolecule #1: the human mPSF complex with FIP1 coordinated by CPSF30 at the CPS...

SupramoleculeName: the human mPSF complex with FIP1 coordinated by CPSF30 at the CPSF160 subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cleavage and polyadenylation specificity factor subunit 1

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 1
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYAVYKQAHP PTGLEFSMYC NFFNNSERNL VVAGTSQLYV YRLNRDAEAL TKNDRSTEGK AHREKLELAA SFSFFGNVMS MASVQLAGAK RDALLLSFKD AKLSVVEYDP GTHDLKTLSL HYFEEPELRD GFVQNVHTPR VRVDPDGRCA AMLVYGTRLV VLPFRRESLA ...String:
MYAVYKQAHP PTGLEFSMYC NFFNNSERNL VVAGTSQLYV YRLNRDAEAL TKNDRSTEGK AHREKLELAA SFSFFGNVMS MASVQLAGAK RDALLLSFKD AKLSVVEYDP GTHDLKTLSL HYFEEPELRD GFVQNVHTPR VRVDPDGRCA AMLVYGTRLV VLPFRRESLA EEHEGLVGEG QRSSFLPSYI IDVRALDEKL LNIIDLQFLH GYYEPTLLIL FEPNQTWPGR VAVRQDTCSI VAISLNITQK VHPVIWSLTS LPFDCTQALA VPKPIGGVVV FAVNSLLYLN QSVPPYGVAL NSLTTGTTAF PLRTQEGVRI TLDCAQATFI SYDKMVISLK GGEIYVLTLI TDGMRSVRAF HFDKAAASVL TTSMVTMEPG YLFLGSRLGN SLLLKYTEKL QEPPASAVRE AADKEEPPSK KKRVDATAGW SAAGKSVPQD EVDEIEVYGS EAQSGTQLAT YSFEVCDSIL NIGPCANAAV GEPAFLSEEF QNSPEPDLEI VVCSGHGKNG ALSVLQKSIR PQVVTTFELP GCYDMWTVIA PVRKEEEDNP KGEGTEQEPS TTPEADDDGR RHGFLILSRE DSTMILQTGQ EIMELDTSGF ATQGPTVFAG NIGDNRYIVQ VSPLGIRLLE GVNQLHFIPV DLGAPIVQCA VADPYVVIMS AEGHVTMFLL KSDSYGGRHH RLALHKPPLH HQSKVITLCL YRDLSGMFTT ESRLGGARDE LGGRSGPEAE GLGSETSPTV DDEEEMLYGD SGSLFSPSKE EARRSSQPPA DRDPAPFRAE PTHWCLLVRE NGTMEIYQLP DWRLVFLVKN FPVGQRVLVD SSFGQPTTQG EARREEATRQ GELPLVKEVL LVALGSRQSR PYLLVHVDQE LLIYEAFPHD SQLGQGNLKV RFKKVPHNIN FREKKPKPSK KKAEGGGAEE GAGARGRVAR FRYFEDIYGY SGVFICGPSP HWLLVTGRGA LRLHPMAIDG PVDSFAPFHN VNCPRGFLYF NRQGELRISV LPAYLSYDAP WPVRKIPLRC TAHYVAYHVE SKVYAVATST NTPCARIPRM TGEEKEFETI ERDERYIHPQ QEAFSIQLIS PVSWEAIPNA RIELQEWEHV TCMKTVSLRS EETVSGLKGY VAAGTCLMQG EEVTCRGRIL IMDVIEVVPE PGQPLTKNKF KVLYEKEQKG PVTALCHCNG HLVSAIGQKI FLWSLRASEL TGMAFIDTQL YIHQMISVKN FILAADVMKS ISLLRYQEES KTLSLVSRDA KPLEVYSVDF MVDNAQLGFL VSDRDRNLMV YMYLPEAKES FGGMRLLRRA DFHVGAHVNT FWRTPCRGAT EGLSKKSVVW ENKHITWFAT LDGGIGLLLP MQEKTYRRLL MLQNALTTML PHHAGLNPRA FRMLHVDRRT LQNAVRNVLD GELLNRYLYL STMERSELAK KIGTTPDIIL DDLLETDRVT AHF

UniProtKB: Cleavage and polyadenylation specificity factor subunit 1

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Macromolecule #2: pre-mRNA 3' end processing protein WDR33

MacromoleculeName: pre-mRNA 3' end processing protein WDR33 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATEIGSPPR FFHMPRFQHQ APRQLFYKRP DFAQQQAMQQ LTFDGKRMRK AVNRKTIDYN PSVIKYLENR IWQRDQRDMR AIQPDAGYYN DLVPPIGMLN NPMNAVTTKF VRTSTNKVKC PVFVVRWTPE GRRLVTGASS GEFTLWNGLT FNFETILQAH DSPVRAMTWS ...String:
MATEIGSPPR FFHMPRFQHQ APRQLFYKRP DFAQQQAMQQ LTFDGKRMRK AVNRKTIDYN PSVIKYLENR IWQRDQRDMR AIQPDAGYYN DLVPPIGMLN NPMNAVTTKF VRTSTNKVKC PVFVVRWTPE GRRLVTGASS GEFTLWNGLT FNFETILQAH DSPVRAMTWS HNDMWMLTAD HGGYVKYWQS NMNNVKMFQA HKEAIREASF SPTDNKFATC SDDGTVRIWD FLRCHEERIL RGHGADVKCV DWHPTKGLVV SGSKDSQQPI KFWDPKTGQS LATLHAHKNT VMEVKLNLNG NWLLTASRDH LCKLFDIRNL KEELQVFRGH KKEATAVAWH PVHEGLFASG GSDGSLLFWH VGVEKEVGGM EMAHEGMIWS LAWHPLGHIL CSGSNDHTSK FWTRNRPGDK MRD

UniProtKB: pre-mRNA 3' end processing protein WDR33

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Macromolecule #3: Cleavage and polyadenylation specificity factor subunit 4

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 4
type: protein_or_peptide / ID: 3 / Details: N-terminal TwinStrep-3C-tag / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KTAGLEVLFQ GPQEIIASVD HIKFDLEIAV EQQLGAQPLP FPGMDKSGAA VCEFFLKAAC GKGGMCPFRH ISGEKTVVCK HWLRGLCKKG DQCEFLHEYD MTKMPECYFY SKFGECSNKE CPFLHIDPES KIKDCPWYDR ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KTAGLEVLFQ GPQEIIASVD HIKFDLEIAV EQQLGAQPLP FPGMDKSGAA VCEFFLKAAC GKGGMCPFRH ISGEKTVVCK HWLRGLCKKG DQCEFLHEYD MTKMPECYFY SKFGECSNKE CPFLHIDPES KIKDCPWYDR GFCKHGPLCR HRHTRRVICV NYLVGFCPEG PSCKFMHPRF ELPMGTTEQP PLPQQTQPPA KQRTPQVIGV MQSQNSSAGN RGPRPLEQVT CYKCGEKGHY ANRCTKGHLA FLSGQ

UniProtKB: Cleavage and polyadenylation specificity factor subunit 4

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Macromolecule #4: Pre-mRNA 3'-end-processing factor FIP1

MacromoleculeName: Pre-mRNA 3'-end-processing factor FIP1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAGEVERLV SELSGGTGGD EEEEWLYGGP WDVHVHSDLA KDLDENEVER PEEENASANP PSGIEDETAE NGVPKPKVTE TEDDSDSDSD DDEDDVHVTI GDIKTGAPQY GSYGTAPVNL NIKTGGRVYG TTGTKVKGVD LDAPGSINGV PLLEVDLDSF EDKPWRKPGA ...String:
MSAGEVERLV SELSGGTGGD EEEEWLYGGP WDVHVHSDLA KDLDENEVER PEEENASANP PSGIEDETAE NGVPKPKVTE TEDDSDSDSD DDEDDVHVTI GDIKTGAPQY GSYGTAPVNL NIKTGGRVYG TTGTKVKGVD LDAPGSINGV PLLEVDLDSF EDKPWRKPGA DLSDYFNYGF NEDTWKAYCE KQKRIRMGLE VIPVTSTTNK ITAEDCTMEV TPGAEIQDGR FNLFKVQQGR TGNSEKETAL PSTKAEFTSP PSLFKTGLPP SRNSTSSQSQ TSTASRKANS SVGKWQDRYG RAESPDLRRL PGAIDVIGQT ITISRVEGRR RANENSNIQV LSERSATEVD NNFSKPPPFF PPGAPPTHLP PPPFLPPPPT VSTAPPLIPP PGF

UniProtKB: Pre-mRNA 3'-end-processing factor FIP1

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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: 7.9
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMC2H3KO2KOAc
1.0 mMC4H6MgO4Mg(OAc)2
1.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 176545
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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