|Entry||Database: PDB / ID: 6fuw|
|Title||Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound to the PAS AAUAAA motif at 3.1 Angstrom resolution|
|Keywords||RNA BINDING PROTEIN / 3' pre-mRNA processing / polyadenylation / CPSF / beta propeller / AAUAAA|
|Function/homology||Zinc-finger containing family / Inhibition of Host mRNA Processing and RNA Silencing / modification by virus of host mRNA processing / mRNA cleavage and polyadenylation specificity factor complex / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Processing of Intronless Pre-mRNAs / mRNA 3'-UTR AU-rich region binding / tRNA splicing, via endonucleolytic cleavage and ligation / pre-mRNA cleavage required for polyadenylation / Zinc finger, CCCH-type superfamily ...Zinc-finger containing family / Inhibition of Host mRNA Processing and RNA Silencing / modification by virus of host mRNA processing / mRNA cleavage and polyadenylation specificity factor complex / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Processing of Intronless Pre-mRNAs / mRNA 3'-UTR AU-rich region binding / tRNA splicing, via endonucleolytic cleavage and ligation / pre-mRNA cleavage required for polyadenylation / Zinc finger, CCCH-type superfamily / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / mRNA 3'-end processing / CPSF A subunit region / Zinc finger C3H1-type profile. / Zinc finger, CCCH-type / Transport of Mature mRNA Derived from an Intronless Transcript / tRNA processing in the nucleus / Cleavage of Growing Transcript in the Termination Region / postreplication repair / mRNA 3'-end processing / collagen trimer / mRNA cleavage / termination of RNA polymerase II transcription / fibrillar center / mRNA export from nucleus / endoribonuclease activity / mRNA polyadenylation / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain / WD40 repeat / WD40-repeat-containing domain superfamily / spermatogenesis / WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc knuckle / Zinc finger CCHC-type profile. / WD domain, G-beta repeat / intracellular membrane-bounded organelle / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / Cleavage and polyadenylation specificity factor subunit 4 / Cleavage and polyadenylation specificity factor subunit 1 / pre-mRNA 3' end processing protein WDR33|
Function and homology information
|Specimen source||Homo sapiens / human / |
unidentified adenovirus / virus
|Method||Electron microscopy (3.07 Å resolution / Particle / Single particle) / Transmission electron microscopy|
|Authors||Clerici, M. / Faini, M. / Jinek, M.|
|Citation||Journal: Nat. Struct. Mol. Biol. / Year: 2018|
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.
|Date||Deposition: Feb 28, 2018 / Release: Mar 21, 2018|
Downloads & links
A: Cleavage and polyadenylation specificity factor subunit 1
B: pre-mRNA 3' end processing protein WDR33
C: Cleavage and polyadenylation specificity factor subunit 4
D: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*GP*G)-3')
|#1: Protein/peptide|| |
Mass: 161346.484 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / / Gene: CPSF1, CPSF160 / Production host: Spodoptera aff. frugiperda 2 RZ-2014 / References: UniProt:Q10570
|#2: Protein/peptide|| |
Mass: 47448.910 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / / Gene: WDR33, WDC146 / Production host: Spodoptera aff. frugiperda 2 RZ-2014 / References: UniProt:Q9C0J8
|#3: Protein/peptide|| |
Mass: 20422.855 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / / Gene: CPSF4, CPSF30, NAR, NEB1 / Production host: Spodoptera aff. frugiperda 2 RZ-2014 / References: UniProt:O95639
|#4: RNA chain|| |
Mass: 3232.036 Da / Num. of mol.: 1 / Source: (synth.) unidentified adenovirus / virus
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Molecular weight||Value: 0.22 deg. / Units: MEGADALTONS / Experimental value: NO|
|Buffer solution||pH: 7.5|
|Specimen||Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 293 kelvins / Details: 15 seconds wait time prior to blotting|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Calibrated magnification: 47259 / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm|
|Specimen holder||Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 10 sec. / Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1070|
|EM imaging optics||Energyfilter name: GIF Quantum LS|
|Image scans||Movie frames/image: 50|
|Software||Name: PHENIX / Version: 1.12_2829: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 263000|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 137000 / Symmetry type: POINT|
|Atomic model building||Details: phenix.real_space_refine / Ref protocol: RIGID BODY FIT / Ref space: REAL|
|Atomic model building||PDB-ID: 6F9N|
Details: fitted manually in Coot
|Least-squares process||Highest resolution: 3.07 Å|
|Refine LS restraints|
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