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Yorodumi- PDB-2peh: Crystal structure of the UHM domain of human SPF45 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2peh | ||||||
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Title | Crystal structure of the UHM domain of human SPF45 in complex with SF3b155-ULM5 | ||||||
Components |
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Keywords | PROTEIN BINDING / RRM / UHM | ||||||
Function / homology | Function and homology information U11/U12 snRNP / B-WICH complex / alternative mRNA splicing, via spliceosome / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / : / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome ...U11/U12 snRNP / B-WICH complex / alternative mRNA splicing, via spliceosome / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / : / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / B-WICH complex positively regulates rRNA expression / mRNA splicing, via spliceosome / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Corsini, L. / Basquin, J. / Hothorn, M. / Sattler, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: U2AF-homology motif interactions are required for alternative splicing regulation by SPF45. Authors: Corsini, L. / Bonna, S. / Basquin, J. / Hothorn, M. / Scheffzek, K. / Valcarcel, J. / Sattler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2peh.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2peh.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 2peh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/2peh ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2peh | HTTPS FTP |
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-Related structure data
Related structure data | 2pe8SC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11690.481 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM17, SPF45 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 BL21(DE3) pLysS / References: UniProt: Q96I25 #2: Protein/peptide | Mass: 1306.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The SF3b 155 peptide was chemically synthesized / References: UniProt: O75533 #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: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% (w/v) PEG 1,500, 0.1 M Malonate, Imidazole, Borate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2006 / Details: mirrors |
Radiation | Monochromator: copper Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→38.3 Å / Num. all: 13008 / Num. obs: 13008 / % possible obs: 89.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.045 / Net I/σ(I): 32.56 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 6.75 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 9.46 / Num. unique all: 1819 / Rsym value: 0.188 / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB-ID 2pe8 Resolution: 2.11→38.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 11.575 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.312 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.339 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→38.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.114→2.169 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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