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Yorodumi- PDB-5osy: Human Decapping Scavenger enzyme (hDcpS) in complex with m7G(5'S)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5osy | |||||||||
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Title | Human Decapping Scavenger enzyme (hDcpS) in complex with m7G(5'S)ppSp(5'S)G mRNA 5' cap analog | |||||||||
Components | m7GpppX diphosphatase | |||||||||
Keywords | HYDROLASE / Protein-ligand complex / decapping / DcpS / m7G(5'S)ppSp(5'S)G / phosphorothiolate / mRNA 5' cap analog / mRNA turnover | |||||||||
Function / homology | Function and homology information mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | |||||||||
Authors | Warminski, M. / Nowak, E. / Wojtczak, B.A. / Fac-Dabrowska, K. / Kubacka, D. / Nowicka, A. / Sikorski, P.J. / Kowalska, J. / Jemielity, J. / Nowotny, M. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: 5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes. Authors: Wojtczak, B.A. / Sikorski, P.J. / Fac-Dabrowska, K. / Nowicka, A. / Warminski, M. / Kubacka, D. / Nowak, E. / Nowotny, M. / Kowalska, J. / Jemielity, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5osy.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5osy.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 5osy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/5osy ftp://data.pdbj.org/pub/pdb/validation_reports/os/5osy | HTTPS FTP |
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-Related structure data
Related structure data | 5osxC 3bl9S 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: 34891.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues 38-337 / Source: (gene. exp.) Homo sapiens (human) / Gene: DCPS, DCS1, HINT5, HSPC015 / Production host: Escherichia coli (E. coli) References: UniProt: Q96C86, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 2.21 Å3/Da / Density % sol: 44.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH 7.6, 31% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 38937 / % possible obs: 99.5 % / Redundancy: 4.37 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.84 |
Reflection shell | Resolution: 2.08→2.16 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 6135 / CC1/2: 0.654 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BL9 Resolution: 2.06→47.787 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 22.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→47.787 Å
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Refine LS restraints |
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LS refinement shell |
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