+Open data
-Basic information
Entry | Database: PDB / ID: 3q2t | ||||||
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Title | Crystal Structure of CFIm68 RRM/CFIm25/RNA complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / CFIm / CFIm25 / CFIm68 / CPSF5 / CPSF6 / CPSF / 3' end processing / RNA processing / cleavage factor / Nudix protein / protein-protein complex / protein-RNA complex / RRM / nudix fold / RNA BINDING PROTEIN-RNA complex | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.061 Å | ||||||
Authors | Yang, Q. / Coseno, M. / Gilmartin, G.M. / Doublie, S. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Crystal Structure of a Human Cleavage Factor CFI(m)25/CFI(m)68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping. Authors: Yang, Q. / Coseno, M. / Gilmartin, G.M. / Doublie, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q2t.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q2t.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 3q2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/3q2t ftp://data.pdbj.org/pub/pdb/validation_reports/q2/3q2t | HTTPS FTP |
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-Related structure data
Related structure data | 3q2sC 3bhoS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24030.703 Da / Num. of mol.: 2 / Fragment: residues 21-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM25, CPSF25, CPSF5, NUDT21 / Plasmid: His6-MBP fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43809 #2: Protein | Mass: 24485.863 Da / Num. of mol.: 2 / Fragment: RRM domain, residues 13-235 / Mutation: C159V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM68, CPSF6 / Plasmid: pET22 C-terminal His6 tag / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q16630 #3: RNA chain | Mass: 1547.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized by Dharmacon #4: 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: 2.21 Å3/Da / Density % sol: 44.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.2M Magnesium Formate, 0.05M HEPES pH 7.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 23, 2010 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MAR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: l,-k,h / Fraction: 0.033 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.06→20 Å / Num. all: 16919 / Num. obs: 16919 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 36.8 % / Rmerge(I) obs: 0.146 / Χ2: 0.998 / Net I/σ(I): 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 3BHO Resolution: 3.061→19.977 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786 Cross valid method: Throughout. Twin based reflections are in the same set σ(F): 0.05 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.161 Å2 / ksol: 0.233 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.66 Å2 / Biso mean: 64.4604 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.061→19.977 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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