+Open data
-Basic information
Entry | Database: PDB / ID: 5vsu | ||||||||||||
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Title | Structure of yeast U6 snRNP with 2'-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 / U4/U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / nuclear-transcribed mRNA catabolic process ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / snRNA binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / U4/U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / spliceosomal snRNP assembly / U6 snRNA binding / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / ribonucleoprotein complex / nucleolus / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||
Authors | Montemayor, E.J. | ||||||||||||
Funding support | United States, 3items
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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 | 5vsu.cif.gz | 251.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vsu.ent.gz | 193.9 KB | Display | PDB format |
PDBx/mmJSON format | 5vsu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/5vsu ftp://data.pdbj.org/pub/pdb/validation_reports/vs/5vsu | HTTPS FTP |
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-Related 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: 11453.212 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: LSM2, SMX5, SNP3, YBL026W, YBL0425 / Production host: Escherichia coli (E. coli) / References: UniProt: P38203 |
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#3: Protein | Mass: 10314.587 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: LSM3, SMX4, USS2, YLR438C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P57743 |
#4: Protein | Mass: 10902.443 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: LSM4, SDB23, USS1, YER112W / Production host: Escherichia coli (E. coli) / References: UniProt: P40070 |
#5: Protein | Mass: 10708.279 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: 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 (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: LSM6, YDR378C, D9481.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06406 |
#7: Protein | Mass: 13302.371 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: LSM7, YNL147W, N1202, N1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P53905 |
#8: Protein | Mass: 12547.507 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: 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: 51998.762 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: PRP24, YMR268C, YM8156.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P49960 |
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#9: RNA chain | Mass: 26695.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: GenBank: 1039023528 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M NH4F 0.1 M HEPES pH 7.4 0.01 M MgCl2 18 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→96.723 Å / Num. obs: 27164 / % possible obs: 100 % / Redundancy: 51.2 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 13 |
Reflection shell | Resolution: 3.1→3.29 Å / Redundancy: 47.7 % / Rmerge(I) obs: 4.031 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→96.723 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 36.28 / 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: 3.1→96.723 Å
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Refine LS restraints |
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LS refinement shell |
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