+Open data
-Basic information
Entry | Database: PDB / ID: 3p5t | ||||||
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Title | CFIm25-CFIm68 complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / RRM domain / Poly(A) site recognition / RNA / nuclear | ||||||
Function / homology | Function and homology information exon-exon junction complex binding / positive regulation of pro-B cell differentiation / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / perichromatin fibrils ...exon-exon junction complex binding / positive regulation of pro-B cell differentiation / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / perichromatin fibrils / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / post-transcriptional regulation of gene expression / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / Signaling by FGFR1 in disease / protein tetramerization / histone deacetylase binding / mRNA processing / cell differentiation / nuclear body / nuclear speck / ribonucleoprotein complex / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Li, H. / Tong, S. / Li, X. / Shi, H. / Gao, Y. / Ge, H. / Niu, L. / Teng, M. | ||||||
Citation | Journal: To be Published Title: Structural basis of pre-mRNA recognition by the human cleavage factor Im complex Authors: Li, H. / Tong, S. / Li, X. / Shi, H. / Gao, Y. / Ge, H. / Niu, L. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p5t.cif.gz | 329.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p5t.ent.gz | 267.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/3p5t ftp://data.pdbj.org/pub/pdb/validation_reports/p5/3p5t | HTTPS FTP |
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-Related structure data
Related structure data | 3p6yC 2cl3S 2fy1S C: citing same article (ref.) S: Starting model for refinement |
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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: 23614.115 Da / Num. of mol.: 6 / Fragment: UNP residues 34-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT21, CFIM25, CPSF25, CPSF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O43809 #2: Protein | Mass: 10149.415 Da / Num. of mol.: 6 / Fragment: UNP residues 80-161 / Mutation: C159S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF6, CFIM68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16630 #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: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 16% PEG 3350, 5% dioxane, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 62054 / Num. obs: 58226 / % possible obs: 98.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.7→2.768 Å / % possible all: 98.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CL3, 2FY1 Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.349 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.363 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.768 Å / Total num. of bins used: 20
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