+Open data
-Basic information
Entry | Database: PDB / ID: 5urm | ||||||
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Title | Crystal structure of human BRR2 in complex with T-1206548 | ||||||
Components | U5 small nuclear ribonucleoprotein 200 kDa helicase | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / BRR2 Inhibitor / RNA helicase / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Klein, M.G. / Tjhen, R. / Qin, L. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Allosteric Inhibitors Targeting the Spliceosomal RNA Helicase Brr2. Authors: Iwatani-Yoshihara, M. / Ito, M. / Klein, M.G. / Yamamoto, T. / Yonemori, K. / Tanaka, T. / Miwa, M. / Morishita, D. / Endo, S. / Tjhen, R. / Qin, L. / Nakanishi, A. / Maezaki, H. / Kawamoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5urm.cif.gz | 688.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5urm.ent.gz | 552.6 KB | Display | PDB format |
PDBx/mmJSON format | 5urm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/5urm ftp://data.pdbj.org/pub/pdb/validation_reports/ur/5urm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 198582.562 Da / Num. of mol.: 2 / Fragment: UNP residues 395-2129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP200, ASCC3L1, HELIC2, KIAA0788 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75643, RNA helicase #2: Chemical | #3: 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: 3.32 Å3/Da / Density % sol: 62.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.25-1.5M sodium malonate, 100mM sodium citrate pH 5.0-5.3, 10mg/ml BRR2 PH range: 5.0-5.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.5 Å / Num. obs: 123431 / % possible obs: 98.2 % / Redundancy: 2.3 % / Net I/σ(I): 8.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.477 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.89 / 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: 2.8→29.477 Å
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Refine LS restraints |
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LS refinement shell |
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