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- EMDB-4225: Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4225 | |||||||||||||||
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Title | Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound to the PAS AAUAAA motif at 3.1 Angstrom resolution. | |||||||||||||||
![]() | Output from Relion2 PostProcess | |||||||||||||||
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Function / homology | ![]() co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-UTR AU-rich region binding / collagen trimer / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / postreplication repair / tRNA processing in the nucleus ...co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-UTR AU-rich region binding / collagen trimer / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / postreplication repair / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / : / Processing of Capped Intron-Containing Pre-mRNA / mRNA processing / fibrillar center / sequence-specific double-stranded DNA binding / spermatogenesis / intracellular membrane-bounded organelle / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||||||||
![]() | Clerici M / Faini M / Jinek M | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Authors: Marcello Clerici / Marco Faini / Lena M Muckenfuss / Ruedi Aebersold / Martin Jinek / ![]() Abstract: Mammalian mRNA biogenesis requires specific recognition of a hexanucleotide AAUAAA motif in the polyadenylation signals (PAS) of precursor mRNA (pre-mRNA) transcripts by the cleavage and ...Mammalian mRNA biogenesis requires specific recognition of a hexanucleotide AAUAAA motif in the polyadenylation signals (PAS) of precursor mRNA (pre-mRNA) transcripts by the cleavage and polyadenylation specificity factor (CPSF) complex. Here we present a 3.1-Å-resolution cryo-EM structure of a core CPSF module bound to the PAS hexamer motif. The structure reveals the molecular interactions responsible for base-specific recognition, providing a rationale for mechanistic differences between mammalian and yeast 3' polyadenylation. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 137.3 KB | ||
Masks | ![]() | 30.5 MB | ![]() | |
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 552.6 KB | Display | ![]() |
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Full document | ![]() | 552.1 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fuwMC ![]() 6fbs M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Output from Relion2 PostProcess | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human CPSF160-WDR33-CPSF30 heterotrimer bound to the AAUAAA motif...
Entire | Name: Human CPSF160-WDR33-CPSF30 heterotrimer bound to the AAUAAA motif of the Polyadenylation Signal |
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Components |
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-Supramolecule #1: Human CPSF160-WDR33-CPSF30 heterotrimer bound to the AAUAAA motif...
Supramolecule | Name: Human CPSF160-WDR33-CPSF30 heterotrimer bound to the AAUAAA motif of the Polyadenylation Signal type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 220 KDa |
-Supramolecule #2: Human CPSF160-WDR33-CPSF30 heterotrimer
Supramolecule | Name: Human CPSF160-WDR33-CPSF30 heterotrimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: AAUAAA motif of the Polyadenylation Signal
Supramolecule | Name: AAUAAA motif of the Polyadenylation Signal / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Cleavage and polyadenylation specificity factor subunit 1
Macromolecule | Name: Cleavage and polyadenylation specificity factor subunit 1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 161.346484 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SNAMYAVYKQ AHPPTGLEFS MYCNFFNNSE RNLVVAGTSQ LYVYRLNRDA EALTKNDRST EGKAHREKLE LAASFSFFGN VMSMASVQL AGAKRDALLL SFKDAKLSVV EYDPGTHDLK TLSLHYFEEP ELRDGFVQNV HTPRVRVDPD GRCAAMLVYG T RLVVLPFR ...String: SNAMYAVYKQ AHPPTGLEFS MYCNFFNNSE RNLVVAGTSQ LYVYRLNRDA EALTKNDRST EGKAHREKLE LAASFSFFGN VMSMASVQL AGAKRDALLL SFKDAKLSVV EYDPGTHDLK TLSLHYFEEP ELRDGFVQNV HTPRVRVDPD GRCAAMLVYG T RLVVLPFR RESLAEEHEG LVGEGQRSSF LPSYIIDVRA LDEKLLNIID LQFLHGYYEP TLLILFEPNQ TWPGRVAVRQ DT CSIVAIS LNITQKVHPV IWSLTSLPFD CTQALAVPKP IGGVVVFAVN SLLYLNQSVP PYGVALNSLT TGTTAFPLRT QEG VRITLD CAQATFISYD KMVISLKGGE IYVLTLITDG MRSVRAFHFD KAAASVLTTS MVTMEPGYLF LGSRLGNSLL LKYT EKLQE PPASAVREAA DKEEPPSKKK RVDATAGWSA AGKSVPQDEV DEIEVYGSEA QSGTQLATYS FEVCDSILNI GPCAN AAVG EPAFLSEEFQ NSPEPDLEIV VCSGHGKNGA LSVLQKSIRP QVVTTFELPG CYDMWTVIAP VRKEEEDNPK GEGTEQ EPS TTPEADDDGR RHGFLILSRE DSTMILQTGQ EIMELDTSGF ATQGPTVFAG NIGDNRYIVQ VSPLGIRLLE GVNQLHF IP VDLGAPIVQC AVADPYVVIM SAEGHVTMFL LKSDSYGGRH HRLALHKPPL HHQSKVITLC LYRDLSGMFT TESRLGGA R DELGGRSGPE AEGLGSETSP TVDDEEEMLY GDSGSLFSPS KEEARRSSQP PADRDPAPFR AEPTHWCLLV RENGTMEIY QLPDWRLVFL VKNFPVGQRV LVDSSFGQPT TQGEARREEA TRQGELPLVK EVLLVALGSR QSRPYLLVHV DQELLIYEAF PHDSQLGQG NLKVRFKKVP HNINFREKKP KPSKKKAEGG GAEEGAGARG RVARFRYFED IYGYSGVFIC GPSPHWLLVT G RGALRLHP MAIDGPVDSF APFHNVNCPR GFLYFNRQGE LRISVLPAYL SYDAPWPVRK IPLRCTAHYV AYHVESKVYA VA TSTNTPC ARIPRMTGEE KEFETIERDE RYIHPQQEAF SIQLISPVSW EAIPNARIEL QEWEHVTCMK TVSLRSEETV SGL KGYVAA GTCLMQGEEV TCRGRILIMD VIEVVPEPGQ PLTKNKFKVL YEKEQKGPVT ALCHCNGHLV SAIGQKIFLW SLRA SELTG MAFIDTQLYI HQMISVKNFI LAADVMKSIS LLRYQEESKT LSLVSRDAKP LEVYSVDFMV DNAQLGFLVS DRDRN LMVY MYLPEAKESF GGMRLLRRAD FHVGAHVNTF WRTPCRGATE GLSKKSVVWE NKHITWFATL DGGIGLLLPM QEKTYR RLL MLQNALTTML PHHAGLNPRA FRMLHVDRRT LQNAVRNVLD GELLNRYLYL STMERSELAK KIGTTPDIIL DDLLETD RV TAHF |
-Macromolecule #2: pre-mRNA 3' end processing protein WDR33
Macromolecule | Name: pre-mRNA 3' end processing protein WDR33 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 47.44891 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SNAMATEIGS PPRFFHMPRF QHQAPRQLFY KRPDFAQQQA MQQLTFDGKR MRKAVNRKTI DYNPSVIKYL ENRIWQRDQR DMRAIQPDA GYYNDLVPPI GMLNNPMNAV TTKFVRTSTN KVKCPVFVVR WTPEGRRLVT GASSGEFTLW NGLTFNFETI L QAHDSPVR ...String: SNAMATEIGS PPRFFHMPRF QHQAPRQLFY KRPDFAQQQA MQQLTFDGKR MRKAVNRKTI DYNPSVIKYL ENRIWQRDQR DMRAIQPDA GYYNDLVPPI GMLNNPMNAV TTKFVRTSTN KVKCPVFVVR WTPEGRRLVT GASSGEFTLW NGLTFNFETI L QAHDSPVR AMTWSHNDMW MLTADHGGYV KYWQSNMNNV KMFQAHKEAI REASFSPTDN KFATCSDDGT VRIWDFLRCH EE RILRGHG ADVKCVDWHP TKGLVVSGSK DSQQPIKFWD PKTGQSLATL HAHKNTVMEV KLNLNGNWLL TASRDHLCKL FDI RNLKEE LQVFRGHKKE ATAVAWHPVH EGLFASGGSD GSLLFWHVGV EKEVGGMEMA HEGMIWSLAW HPLGHILCSG SNDH TSKFW TRNRPGDK |
-Macromolecule #3: Cleavage and polyadenylation specificity factor subunit 4
Macromolecule | Name: Cleavage and polyadenylation specificity factor subunit 4 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.422855 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MQEIIASVDH IKFDLEIAVE QQLGAQPLPF PGMDKSGAAV CEFFLKAACG KGGMCPFRHI SGEKTVVCKH WLRGLCKKGD QCEFLHEYD MTKMPECYFY SKFGECSNKE CPFLHIDPES KIKDCPWYDR GFCKHGPLCR HRHTRRVICV NYLVGFCPEG P SCKFMHPR FELPMGTTEQ |
-Macromolecule #4: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*GP*G)-3')
Macromolecule | Name: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*GP*G)-3') / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.232036 KDa |
Sequence | String: ACAAUAAAGG |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: 15 seconds wait time prior to blotting. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1070 / Average exposure time: 10.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 47259 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |