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Yorodumi- PDB-3mdi: Crystal Structure of the 25kDa Subunit of Human Cleavage factor I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mdi | ||||||
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Title | Crystal Structure of the 25kDa Subunit of Human Cleavage factor Im in complex with RNA UGUAAA | ||||||
Components |
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Keywords | RNA binding/RNA / CPSF5 / CF Im / mRNA processing / cleavage factor / Nudix protein / protein-RNA complex / RNA binding protein / RNA binding-RNA complex | ||||||
Function / homology | Function and homology information positive regulation of pro-B cell differentiation / : / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-UTR AU-rich region binding / paraspeckles / mRNA 3'-end processing ...positive regulation of pro-B cell differentiation / : / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-UTR AU-rich region binding / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / protein heterotetramerization / post-transcriptional regulation of gene expression / : / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / protein tetramerization / mRNA processing / histone deacetylase binding / cell differentiation / nuclear body / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Yang, Q. / Gilmartin, G.M. / Doublie, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing. Authors: Yang, Q. / 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 | 3mdi.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mdi.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/3mdi ftp://data.pdbj.org/pub/pdb/validation_reports/md/3mdi | HTTPS FTP |
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-Related structure data
Related structure data | 3mdgC 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: 26259.242 Da / Num. of mol.: 2 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: RNA chain | | Mass: 1900.197 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 25% PEG 8000, 0.2M Sodium phosphate pH 4.9, 0.1M Sodium acetate pH 5.0, 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: Jul 31, 2009 / 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: k,h,-l / Fraction: 0.074 |
Reflection | Resolution: 2.07→20 Å / Num. obs: 30752 / % possible obs: 99.511 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.081 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.82 |
Reflection shell | Resolution: 2.07→2.15 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 35077 / Num. unique all: 6307 / Num. unique obs: 6086 / % possible all: 87.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BHO Resolution: 2.07→19.937 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.821 / Cross valid method: THROUGHOUT / σ(F): 1.55 / Stereochemistry target values: TWIN_LSQ_F / Details: Twin law: k,h,-l, Twin percentage 0.074
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.575 Å2 / ksol: 0.399 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.27 Å2 / Biso mean: 26.139 Å2 / Biso min: 10.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→19.937 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: 20
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