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Yorodumi- PDB-4ru2: Crystal structure of a RNA-binding protein 39 (RBM39) in complex ... -
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-Basic information
Entry | Database: PDB / ID: 4ru2 | ||||||
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Title | Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / RBM39linker (PF15519) / RNA recognition motif (PF13893) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL | ||||||
Function / homology | Function and homology information Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / Initiation of Nuclear Envelope (NE) Reformation / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / RND3 GTPase cycle / Protein hydroxylation / RS domain binding / RAC3 GTPase cycle ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / Initiation of Nuclear Envelope (NE) Reformation / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / RND3 GTPase cycle / Protein hydroxylation / RS domain binding / RAC3 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / mRNA Splicing - Major Pathway / U2AF complex / RND2 GTPase cycle / RND1 GTPase cycle / RAC1 GTPase cycle / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / RHOG GTPase cycle / Prp19 complex / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / commitment complex / U2-type prespliceosome / spliceosomal complex assembly / negative regulation of mRNA splicing, via spliceosome / centriolar satellite / negative regulation of protein ubiquitination / RNA splicing / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / enzyme binding / protein-containing complex / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ru2.cif.gz | 450.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ru2.ent.gz | 372.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ru2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ru2_validation.pdf.gz | 502.5 KB | Display | wwPDB validaton report |
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Full document | 4ru2_full_validation.pdf.gz | 504.5 KB | Display | |
Data in XML | 4ru2_validation.xml.gz | 43 KB | Display | |
Data in CIF | 4ru2_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/4ru2 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/4ru2 | HTTPS FTP |
-Related structure data
Related structure data | 3s6eS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12622.324 Da / Num. of mol.: 9 / Fragment: UNP residues 418-530 / Mutation: N468Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: CAPER, RBM39, RNPC2, WS20613E / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8VH51 #2: Protein/peptide | Mass: 3439.078 Da / Num. of mol.: 9 / Fragment: UNP residues 85-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: U2AF2, U2AF65, WT4514D / Plasmid: pGEX4T / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: P26369 #3: Water | ChemComp-HOH / | Sequence details | THE CRYSTAL STRUCTURE CONSISTS OF TWO DIFFERENT CONSTRUCTS. BOTH CONSTRUCTS WERE EXPRESSED WITH AN ...THE CRYSTAL STRUCTURE CONSISTS OF TWO DIFFERENT CONSTRUCTS | |
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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: 2.55 Å3/Da / Density % sol: 51.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M potassium chloride, 15.0% polyethylene glycol monomethyl ether 5000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2013 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→39.432 Å / Num. obs: 72455 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.71 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3S6E Resolution: 2.2→39.432 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2.NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION ...Details: 1.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2.NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 3.DURING REFINEMENT, SIDECHAIN TYR468 ON THE A,E,G,I,K,M,O AND Q SUBUNITS MOVED OUT OF DENSITY. TO IMPROVE THE FIT OF THESE TYR468 SIDECHAINS TO THEIR ELECTRON DENSITIES SOME VAN DER WAALS CONTACT RESTRAINTS BETWEEN THESE TYR468 RESIDUES AND SOME NEARBY RESIDUES AND WATER MOLECULES WERE EXCLUDED FROM THE REFINEMENT.
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Displacement parameters | Biso max: 148.55 Å2 / Biso mean: 43.298 Å2 / Biso min: 12.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.432 Å
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LS refinement shell | Resolution: 2.2→2.26 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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