+Open data
-Basic information
Entry | Database: PDB / ID: 6en4 | ||||||
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Title | SF3b core in complex with a splicing modulator | ||||||
Components |
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Keywords | SPLICING / Protein complex / splicing modulator | ||||||
Function / homology | Function and homology information U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / regulation of DNA repair / U2 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA splicing, via spliceosome / nuclear matrix / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||
Authors | Cretu, C. / Pena, V. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Mol. Cell / Year: 2018 Title: Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Authors: Cretu, C. / Agrawal, A.A. / Cook, A. / Will, C.L. / Fekkes, P. / Smith, P.G. / Luhrmann, R. / Larsen, N. / Buonamici, S. / Pena, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6en4.cif.gz | 447 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6en4.ent.gz | 350.6 KB | Display | PDB format |
PDBx/mmJSON format | 6en4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/6en4 ftp://data.pdbj.org/pub/pdb/validation_reports/en/6en4 | HTTPS FTP |
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-Related structure data
Related structure data | 5ifeS S: Starting model for refinement |
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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
-Splicing factor 3B subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 135018.984 Da / Num. of mol.: 1 / Mutation: internal deletion 1068-1085 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B3, KIAA0017, SAP130 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15393 |
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#2: Protein | Mass: 10018.173 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B5, SF3B10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BWJ5 |
#3: Protein | Mass: 96615.734 Da / Num. of mol.: 1 / Mutation: deletion 1-452 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B1, SAP155 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75533 |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 11670.525 Da / Num. of mol.: 1 / Mutation: deletion 99-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHF5A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7RTV0 |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | ChemComp-BGZ / [( | |
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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: 3.4 Å3/Da / Density % sol: 63.83 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 50 mM HEPES-NaOH, pH 7-7.4, 200 mM KCl, and 38-39% (v/v) pentaerythritol propoxylate (5/4 PO/OH) PH range: 7.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→48.79 Å / Num. obs: 64636 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 1 / Net I/σ(I): 16.85 |
Reflection shell | Resolution: 3.08→3.19 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6273 / CC1/2: 0.556 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IFE Resolution: 3.08→48.79 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.08→48.79 Å
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