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- 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 | ||||||
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![]() | 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 | ![]() Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / 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 / Protein hydroxylation / RAC3 GTPase cycle / RS domain binding ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / 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 / Protein hydroxylation / RAC3 GTPase cycle / RS domain binding / RAC2 GTPase cycle / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle / U2AF complex / RND2 GTPase cycle / RND1 GTPase cycle / RHOG GTPase cycle / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Prp19 complex / U1 snRNP binding / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / 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 processing / mRNA splicing, via spliceosome / nuclear speck / enzyme binding / protein-containing complex / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 450.5 KB | Display | ![]() |
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PDB format | ![]() | 372.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.5 KB | Display | ![]() |
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Full document | ![]() | 504.5 KB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 61.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s6eS S: Starting model for refinement |
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Similar structure data | |
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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.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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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