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- EMDB-14712: Polymerase module of yeast CPF in complex with Mpe1, the yPIM of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14712
TitlePolymerase module of yeast CPF in complex with Mpe1, the yPIM of Cft2 and the pre-cleaved CYC1 RNA
Map data
Sample
  • Complex: polymerase module-Mpe1-yPIM-RNA
    • Protein or peptide: Protein CFT1
    • Protein or peptide: mRNA 3'-end-processing protein YTH1
    • Protein or peptide: Cleavage factor two protein 2
    • Protein or peptide: Polyadenylation factor subunit 2
    • RNA: pre-cleaved CYC1
    • Protein or peptide: MPE1 isoform 1
  • Ligand: ZINC ION
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / termination of RNA polymerase II transcription, poly(A)-coupled / intracellular organelle / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / : / mRNA processing / ubiquitin protein ligase activity / nucleic acid binding ...Processing of Intronless Pre-mRNAs / termination of RNA polymerase II transcription, poly(A)-coupled / intracellular organelle / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / : / mRNA processing / ubiquitin protein ligase activity / nucleic acid binding / mitochondrion / RNA binding / zinc ion binding / metal ion binding / nucleus
Similarity search - Function
E3 ubiquitin-protein ligase RBBP6 family / DWNN domain / DWNN domain / DWNN domain profile. / DWNN / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / CPSF complex subunit CPSF4-like ...E3 ubiquitin-protein ligase RBBP6 family / DWNN domain / DWNN domain / DWNN domain profile. / DWNN / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / CPSF complex subunit CPSF4-like / RNA-binding, Nab2-type zinc finger / Pre-mRNA 3' end processing protein Pfs2-like / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
MPE1 isoform 1 / mRNA 3'-end-processing protein / Polyadenylation factor subunit 2 / Protein CFT1 / Cleavage factor two protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsRodriguez-Molina JB / Passmore LA
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)725685European Union
Medical Research Council (MRC, United Kingdom)MC_U105192715 United Kingdom
CitationJournal: Mol Cell / Year: 2022
Title: Mpe1 senses the binding of pre-mRNA and controls 3' end processing by CPF.
Authors: Juan B Rodríguez-Molina / Francis J O'Reilly / Holly Fagarasan / Eleanor Sheekey / Sarah Maslen / J Mark Skehel / Juri Rappsilber / Lori A Passmore /
Abstract: Most eukaryotic messenger RNAs (mRNAs) are processed at their 3' end by the cleavage and polyadenylation specificity factor (CPF/CPSF). CPF mediates the endonucleolytic cleavage of the pre-mRNA and ...Most eukaryotic messenger RNAs (mRNAs) are processed at their 3' end by the cleavage and polyadenylation specificity factor (CPF/CPSF). CPF mediates the endonucleolytic cleavage of the pre-mRNA and addition of a polyadenosine (poly(A)) tail, which together define the 3' end of the mature transcript. The activation of CPF is highly regulated to maintain the fidelity of RNA processing. Here, using cryo-EM of yeast CPF, we show that the Mpe1 subunit directly contacts the polyadenylation signal sequence in nascent pre-mRNA. The region of Mpe1 that contacts RNA also promotes the activation of CPF endonuclease activity and controls polyadenylation. The Cft2 subunit of CPF antagonizes the RNA-stabilized configuration of Mpe1. In vivo, the depletion or mutation of Mpe1 leads to widespread defects in transcription termination by RNA polymerase II, resulting in transcription interference on neighboring genes. Together, our data suggest that Mpe1 plays a major role in accurate 3' end processing, activating CPF, and ensuring timely transcription termination.
History
DepositionApr 4, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14712.png

Downloads & links

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Map

FileDownload / File: emd_14712.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.029737283 - 0.06973583
Average (Standard dev.)3.2639957e-05 (±0.0019224613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14712_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14712_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : polymerase module-Mpe1-yPIM-RNA

EntireName: polymerase module-Mpe1-yPIM-RNA
Components
  • Complex: polymerase module-Mpe1-yPIM-RNA
    • Protein or peptide: Protein CFT1
    • Protein or peptide: mRNA 3'-end-processing protein YTH1
    • Protein or peptide: Cleavage factor two protein 2
    • Protein or peptide: Polyadenylation factor subunit 2
    • RNA: pre-cleaved CYC1
    • Protein or peptide: MPE1 isoform 1
  • Ligand: ZINC ION

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Supramolecule #1: polymerase module-Mpe1-yPIM-RNA

SupramoleculeName: polymerase module-Mpe1-yPIM-RNA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Protein CFT1

MacromoleculeName: Protein CFT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 153.577156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNVYDDVLDA TVVSHSLATH FTTSDYEELL VVRTNILSVY RPTRDGKLYL TDEFKFHGLI TDIGLIPQKD SPLSCLLLCT GVAKISILK FNTLTNSIDT LSLHYYEGKF KGKSLVELAK ISTLRMDPGS SCALLFNNDI IAFLPFHVNK NDDDEEEEDE D ENIDDSEL ...String:
MNVYDDVLDA TVVSHSLATH FTTSDYEELL VVRTNILSVY RPTRDGKLYL TDEFKFHGLI TDIGLIPQKD SPLSCLLLCT GVAKISILK FNTLTNSIDT LSLHYYEGKF KGKSLVELAK ISTLRMDPGS SCALLFNNDI IAFLPFHVNK NDDDEEEEDE D ENIDDSEL IHSMNQKSQG TNTFNKRKRT KLGDKFTAPS VVLVASELYE GAKNIIDIQF LKNFTKPTIA LLYQPKLVWA GN TTISKLP TQYVILTLNI QPAESATKIE STTIAFVKEL PWDLHTIVPV SNGAIIVGTN ELAFLDNTGV LQSTVLLNSF ADK ELQKTK IINNSSLEIM FREKNTTSIW IPSSKSKNGG SNNDETLLLM DLKSNIYYIQ MEAEGRLLIK FDIFKLPIVN DLLK ENSNP KCITRLNATN SNKNMDLFIG FGSGNALVLR LNNLKSTIET REAHNPSSGT NSLMDINDDD DEEMDDLYAD EAPEN GLTT NDSKGTVETV QPFDIELLSS LRNVGPITSL TVGKVSSIDD VVKGLPNPNK NEYSLVATSG NGSGSHLTVI QTSVQP EIE LALKFISITQ IWNLKIKGRD RYLITTDSTK SRSDIYESDN NFKLHKGGRL RRDATTVYIS MFGEEKRIIQ VTTNHLY LY DTHFRRLTTI KFDYEVIHVS VMDPYILVTV SRGDIKIFEL EEKNKRKLLK VDLPEILNEM VITSGLILKS NMCNEFLI G LSKSQEEQLL FTFVTADNQI IFFTKDHNDR IFQLNGVDQL NESLYISTYQ LGDEIVPDPS IKQVMINKLG HDNKEEYLT ILTFGGEIYQ YRKLPQRRSR FYRNVTRNDL AITGAPDNAY AKGVSSIERI MHYFPDYNGY SVIFVTGSVP YILIKEDDST PKIFKFGNI PLVSVTPWSE RSVMCVDDIK NARVYTLTTD NMYYGNKLPL KQIKISNVLD DYKTLQKLVY HERAQLFLVS Y CKRVPYEA LGEDGEKVIG YDENVPHAEG FQSGILLINP KSWKVIDKID FPKNSVVNEM RSSMIQINSK TKRKREYIIA GV ANATTED TPPTGAFHIY DVIEVVPEPG KPDTNYKLKE IFQEEVSGTV STVCEVSGRF MISQSQKVLV RDIQEDNSVI PVA FLDIPV FVTDSKSFGN LLIIGDAMQG FQFIGFDAEP YRMISLGRSM SKFQTMSLEF LVNGGDMYFA ATDADRNVHV LKYA PDEPN SLSGQRLVHC SSFTLHSTNS CMMLLPRNEE FGSPQVPSFQ NVGGQVDGSV FKIVPLSEEK YRRLYVIQQQ IIDRE LQLG GLNPRMERLA NDFYQMGHSM RPMLDFNVIR RFCGLAIDRR KSIAQKAGRH AHFEAWRDII NIEFSMRSLC QGK

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Macromolecule #2: mRNA 3'-end-processing protein YTH1

MacromoleculeName: mRNA 3'-end-processing protein YTH1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.594498 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLIHPDTAK YPFKFEPFLR QEYSFSLDPD RPICEFYNSR EGPKSCPRGP LCPKKHVLPI FQNKIVCRHW LRGLCKKNDQ CEYLHEYNL RKMPECVFFS KNGYCTQSPD CQYLHIDPAS KIPKCENYEM GFCPLGSSCP RRHIKKVFCQ RYMTGFCPLG K DECDMEHP ...String:
MSLIHPDTAK YPFKFEPFLR QEYSFSLDPD RPICEFYNSR EGPKSCPRGP LCPKKHVLPI FQNKIVCRHW LRGLCKKNDQ CEYLHEYNL RKMPECVFFS KNGYCTQSPD CQYLHIDPAS KIPKCENYEM GFCPLGSSCP RRHIKKVFCQ RYMTGFCPLG K DECDMEHP QFIIPDEGSK LRIKRDDEIN TRKMDEEKER RLNAIINGEV

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Macromolecule #3: Cleavage factor two protein 2

MacromoleculeName: Cleavage factor two protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 80.993055 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTYKYNCCDD GSGTTVGSVV RFDNVTLLID PGWNPSKVSY EQCIKYWEKV IPEIDVIILS QPTIECLGAH SLLYYNFTSH FISRIQVYA TLPVINLGRV STIDSYASAG VIGPYDTNKL DLEDIEISFD HIVPLKYSQL VDLRSRYDGL TLLAYNAGVC P GGSIWCIS ...String:
MTYKYNCCDD GSGTTVGSVV RFDNVTLLID PGWNPSKVSY EQCIKYWEKV IPEIDVIILS QPTIECLGAH SLLYYNFTSH FISRIQVYA TLPVINLGRV STIDSYASAG VIGPYDTNKL DLEDIEISFD HIVPLKYSQL VDLRSRYDGL TLLAYNAGVC P GGSIWCIS TYSEKLVYAK RWNHTRDNIL NAASILDATG KPLSTLMRPS AIITTLDRFG SSQPFKKRSK IFKDTLKKGL SS DGSVIIP VDMSGKFLDL FTQVHELLFE STKINAHTQV PVLILSYARG RTLTYAKSML EWLSPSLLKT WENRNNTSPF EIG SRIKII APNELSKYPG SKICFVSEVG ALINEVIIKV GNSEKTTLIL TKPSFECASS LDKILEIVEQ DERNWKTFPE DGKS FLCDN YISIDTIKEE PLSKEETEAF KVQLKEKKRD RNKKILLVKR ESKKLANGNA IIDDTNGERA MRNQDILVEN VNGVP PIDH IMGGDEDDDE EEENDNLLNL LKDNSEKSAA KKNTEVPVDI IIQPSAASKH KMFPFNPAKI KKDDYGTVVD FTMFLP DDS DNVNQNSRKR PLKDGAKTTS PVNEEDNKNE EEDGYNMSDP ISKRSKHRAS RYSGFSGTGE AENFDNLDYL KIDKTLS KR TISTVNVQLK CSVVILNLQS LVDQRSASII WPSLKSRKIV LSAPKQIQNE EITAKLIKKN IEVVNMPLNK IVEFSTTI

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Macromolecule #4: Polyadenylation factor subunit 2

MacromoleculeName: Polyadenylation factor subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 53.211117 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDGHNQNQYQ NQNQIQQSQQ PPLKKYVTQR RSVDVSSPYI NLYYNRRHGL PNLVVEPETS YTIDIMPPNA YRGRDRVINL PSKFTHLSS NKVKHVIPAI QWTPEGRRLV VATYSGEFSL WNASSFTFET LMQAHDSAVT TMKYSHDSDW MISGDADGMI K IWQPNFSM ...String:
MDGHNQNQYQ NQNQIQQSQQ PPLKKYVTQR RSVDVSSPYI NLYYNRRHGL PNLVVEPETS YTIDIMPPNA YRGRDRVINL PSKFTHLSS NKVKHVIPAI QWTPEGRRLV VATYSGEFSL WNASSFTFET LMQAHDSAVT TMKYSHDSDW MISGDADGMI K IWQPNFSM VKEIDAAHTE SIRDMAFSSN DSKFVTCSDD NILKIWNFSN GKQERVLSGH HWDVKSCDWH PEMGLIASAS KD NLVKLWD PRSGNCISSI LKFKHTVLKT RFQPTKGNLL MAISKDKSCR VFDIRYSMKE LMCVRDETDY MTLEWHPINE SMF TLACYD GSLKHFDLLQ NLNEPILTIP YAHDKCITSL SYNPVGHIFA TAAKDRTIRF WTRARPIDPN AYDDPTYNNK KING WFFGI NNDINAVREK SEFGAAPPPP ATLEPHALPN MNGFINKKPR QEIPGIDSNI KSSTLPGLSI

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Macromolecule #6: MPE1 isoform 1

MacromoleculeName: MPE1 isoform 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 49.711848 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSTIFYRFK SQRNTSRILF DGTGLTVFDL KREIIQENKL GDGTDFQLKI YNPDTEEEYD DDAFVIPRST SVIVKRSPAI KSFSVHSRL KGNVGAAALG NATRYVTGRP RVLQKRQHTA TTTANVSGTT EEERIASMFA TQENQWEQTQ EEMSAATPVF F KSQTNKNS ...String:
MSSTIFYRFK SQRNTSRILF DGTGLTVFDL KREIIQENKL GDGTDFQLKI YNPDTEEEYD DDAFVIPRST SVIVKRSPAI KSFSVHSRL KGNVGAAALG NATRYVTGRP RVLQKRQHTA TTTANVSGTT EEERIASMFA TQENQWEQTQ EEMSAATPVF F KSQTNKNS AQENEGPPPP GYMCYRCGGR DHWIKNCPTN SDPNFEGKRI RRTTGIPKKF LKSIEIDPET MTPEEMAQRK IM ITDEGKF VVQVEDKQSW EDYQRKRENR QIDGDETIWR KGHFKDLPDD LKCPLTGGLL RQPVKTSKCC NIDFSKEALE NAL VESDFV CPNCETRDIL LDSLVPDQDK EKEVETFLKK QEELHGSSKD GNQPETKKMK LMDPTGTAGL NNNTSLPTSV NNGG TPVPP VPLPFGIPPF PMFPMPFMPP TATITNPHQA DASPKK

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Macromolecule #5: pre-cleaved CYC1

MacromoleculeName: pre-cleaved CYC1 / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.329796 KDa
SequenceString:
UUUAUAGUUA UGUUAGUAUU AAGAACGUUA UUUAUAUUUC AA

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 8 / Details: 20 mM HEPES pH 8, 50 mM NaCl, 0.5 mM TCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 19524 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13905256
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

3908

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 846349

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Atomic model buiding 1

Initial model(PDB ID:

7zgp

,

1zgq

)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7zgr:
Polymerase module of yeast CPF in complex with Mpe1, the yPIM of Cft2 and the pre-cleaved CYC1 RNA

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