+Open data
-Basic information
Entry | Database: PDB / ID: 6i1d | ||||||||||||
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Title | Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae | ||||||||||||
Components |
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Keywords | GENE REGULATION / pre-mRNA / mRNA / nuclease / endonuclease / cleavage / polyadenylation / polyA / CPF / metallo-beta-lactamase / 3' ends | ||||||||||||
Function / homology | Function and homology information : / : / Processing of Intronless Pre-mRNAs / sno(s)RNA 3'-end processing / snoRNA splicing / mRNA cleavage and polyadenylation specificity factor complex / Antigen processing: Ubiquitination & Proteasome degradation / 5'-3' exonuclease activity / pre-mRNA binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters ...: / : / Processing of Intronless Pre-mRNAs / sno(s)RNA 3'-end processing / snoRNA splicing / mRNA cleavage and polyadenylation specificity factor complex / Antigen processing: Ubiquitination & Proteasome degradation / 5'-3' exonuclease activity / pre-mRNA binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / : / termination of RNA polymerase II transcription / RNA endonuclease activity / RNA splicing / protein polyubiquitination / ubiquitin protein ligase activity / protein ubiquitination / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||||||||
Authors | Hill, C.H. / Boreikaite, V. / Kumar, A. / Casanal, A. / Kubik, P. / Degliesposti, G. / Maslen, S. / Mariani, A. / von Loeffelholz, O. / Girbig, M. ...Hill, C.H. / Boreikaite, V. / Kumar, A. / Casanal, A. / Kubik, P. / Degliesposti, G. / Maslen, S. / Mariani, A. / von Loeffelholz, O. / Girbig, M. / Skehel, M. / Passmore, L.A. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Mol Cell / Year: 2019 Title: Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex. Authors: Chris H Hill / Vytautė Boreikaitė / Ananthanarayanan Kumar / Ana Casañal / Peter Kubík / Gianluca Degliesposti / Sarah Maslen / Angelica Mariani / Ottilie von Loeffelholz / Mathias ...Authors: Chris H Hill / Vytautė Boreikaitė / Ananthanarayanan Kumar / Ana Casañal / Peter Kubík / Gianluca Degliesposti / Sarah Maslen / Angelica Mariani / Ottilie von Loeffelholz / Mathias Girbig / Mark Skehel / Lori A Passmore / Abstract: Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The ...Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPF" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPF. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i1d.cif.gz | 243.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i1d.ent.gz | 194.2 KB | Display | PDB format |
PDBx/mmJSON format | 6i1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/6i1d ftp://data.pdbj.org/pub/pdb/validation_reports/i1/6i1d | HTTPS FTP |
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-Related structure data
Related structure data | 0324C 0325C 2c7hS 2i7vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53458.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: YSH1, BRR5, YLR277C / Cell line (production host): Sf9 / Production host: unidentified baculovirus References: UniProt: Q06224, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters | ||||
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#2: Protein | Mass: 18075.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MPE1, YKL059C, YKL316 / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: P35728 | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % / Description: plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 Details: 80 ul reservoir of 26 % w/v PEG 3000, 0.1 M CHES pH 8.7 The final drop of 400 nl comprised 200 nl protein and 200 nl crystallization buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→62.13 Å / Num. obs: 29524 / % possible obs: 99.08 % / Redundancy: 3.39 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.28→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1442 / CC1/2: 0.578 / Rpim(I) all: 0.716 / Rrim(I) all: 1.346 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I7V, 2C7H Resolution: 2.28→62.135 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→62.135 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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