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Yorodumi- PDB-8bca: Human Brr2 Helicase Region in complex with C-tail deleted Jab1 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bca | ||||||
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Title | Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 26 | ||||||
Components |
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Keywords | HYDROLASE / helicase / complex / 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 / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 8bca.cif.gz | 977.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bca.ent.gz | 668.9 KB | Display | PDB format |
PDBx/mmJSON format | 8bca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bca_validation.pdf.gz | 973.7 KB | Display | wwPDB validaton report |
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Full document | 8bca_full_validation.pdf.gz | 1005.4 KB | Display | |
Data in XML | 8bca_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 8bca_validation.cif.gz | 98.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/8bca ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bca | HTTPS FTP |
-Related structure data
Related structure data | 8bc8C 8bc9C 8bcbC 8bccC 8bcdC 8bceC 8bcfC 8bcgC 8bchC 6s8qS 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
-Protein , 2 types, 2 molecules BJ
#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: Protein | Mass: 30133.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF8, PRPC8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P2Q9 |
-Non-polymers , 4 types, 185 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Hepes-NaOH, 0.1M MgCl2, 8% PEG 3350 |
-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: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 56042 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 66.51 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.22 / Net I/σ(I): 8.05 |
Reflection shell | Resolution: 2.8→2.97 Å / Mean I/σ(I) obs: 8.05 / Num. unique obs: 8857 / CC1/2: 0.374 / Rrim(I) all: 0.22 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S8Q Resolution: 2.8→48.53 Å / SU ML: 0.4404 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8141 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: 78.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.53 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
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