+Open data
-Basic information
Entry | Database: PDB / ID: 6aso | |||||||||
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Title | Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA | |||||||||
Components |
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Keywords | SPLICING / Lsm2-8 spliceosome U6 Prp24 | |||||||||
Function / homology | Function and homology information mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / snRNA binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / tRNA processing ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / snRNA binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / tRNA processing / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | |||||||||
Authors | Montemayor, E.J. / Brow, D.A. / Butcher, S.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA. Authors: Montemayor, E.J. / Didychuk, A.L. / Yake, A.D. / Sidhu, G.K. / Brow, D.A. / Butcher, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aso.cif.gz | 368 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aso.ent.gz | 292.2 KB | Display | PDB format |
PDBx/mmJSON format | 6aso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aso_validation.pdf.gz | 538.6 KB | Display | wwPDB validaton report |
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Full document | 6aso_full_validation.pdf.gz | 574.3 KB | Display | |
Data in XML | 6aso_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 6aso_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/6aso ftp://data.pdbj.org/pub/pdb/validation_reports/as/6aso | HTTPS FTP |
-Related structure data
Related structure data | 5vsuSC 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
-U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules BCDEFGH
#2: Protein | Mass: 11177.888 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM2, SMX5, SNP3, YBL026W, YBL0425 / Production host: Escherichia coli (E. coli) / References: UniProt: P38203 |
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#3: Protein | Mass: 11081.407 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM3, SMX4, USS2, YLR438C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P57743 |
#4: Protein | Mass: 10627.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM4, SDB23, USS1, YER112W / Production host: Escherichia coli (E. coli) / References: UniProt: P40070 |
#5: Protein | Mass: 10432.954 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM5, YER146W / Production host: Escherichia coli (E. coli) / References: UniProt: P40089 |
#6: Protein | Mass: 9550.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YJM789 / Gene: LSM6, SCY_1265 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZYX7 |
#7: Protein | Mass: 13027.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM7, YNL147W, N1202, N1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P53905 |
#8: Protein | Mass: 13232.260 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM8, YJR022W, J1464, YJR83.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P47093 |
-Protein / RNA chain , 2 types, 2 molecules AI
#1: Protein | Mass: 49049.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRP24, YMR268C, YM8156.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P49960 |
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#9: RNA chain | Mass: 27017.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039023481 |
-Non-polymers , 4 types, 139 molecules
#10: Chemical | #11: Chemical | ChemComp-MN / | #12: Chemical | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 280 mM sodium potassium tartrate 22.5 % glycerol 17.5 % PEG 3,350 1 mM manganese chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.711→90.59 Å / Num. obs: 40745 / % possible obs: 100 % / Redundancy: 60.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.446 / Rpim(I) all: 0.058 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 58.5 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4574 / CC1/2: 0.418 / Rpim(I) all: 2.18 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VSU Resolution: 2.71→55.63 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→55.63 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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