+Open data
-Basic information
Entry | Database: PDB / ID: 8bch | ||||||
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Title | Human Brr2 Helicase Region in complex with Sulfaguanidine | ||||||
Components | U5 small nuclear ribonucleoprotein 200 kDa helicase | ||||||
Keywords | HYDROLASE / helicase / ligand | ||||||
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: 2.87 Å | ||||||
Authors | Vester, K. / Loll, B. / Wahl, M.C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2. Authors: Vester, K. / Metz, A. / Huber, S. / Loll, B. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bch.cif.gz | 849.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bch.ent.gz | 587 KB | Display | PDB format |
PDBx/mmJSON format | 8bch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/8bch ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bch | HTTPS FTP |
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-Related structure data
Related structure data | 8bc8C 8bc9C 8bcaC 8bcbC 8bccC 8bcdC 8bceC 8bcfC 8bcgC 4f91S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 199666.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP200, ASCC3L1, HELIC2, KIAA0788 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75643, RNA helicase |
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#2: Chemical | ChemComp-QA9 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.23 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium citrate, 1.5M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→50 Å / Num. obs: 58705 / % possible obs: 97.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 82.9 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.201 / Net I/σ(I): 10.19 |
Reflection shell | Resolution: 2.87→3.04 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.63 / Num. unique obs: 9524 / CC1/2: 0.38 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F91 Resolution: 2.87→47.2 Å / SU ML: 0.7015 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 46.6319 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→47.2 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A
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