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Yorodumi- PDB-2j8q: Crystal structure of human cleavage and polyadenylation specifici... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j8q | ||||||
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Title | Crystal structure of human cleavage and polyadenylation specificity factor 5 (CPSF5) in complex with a sulphate ion. | ||||||
Components | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5 | ||||||
Keywords | NUCLEAR PROTEIN / RNA-BINDING / MRNA PROCESSING / PHOSPHORYLATION / 3'MRNA CLEAVAGE AND POLYADENYLATION FACTOR | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Moche, M. / Stenmark, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. ...Moche, M. / Stenmark, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg, S.L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Magnusdottir, A. / Nilsson, M.E. / Nilsson-Ehle, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Welin, M. / Nordlund, P. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: The Crystal Structure of Human Cleavage and Polyadenylation Specific Factor-5 Reveals a Dimeric Nudix Protein with a Conserved Catalytic Site. Authors: Tresaugues, L. / Stenmark, P. / Schuler, H. / Flodin, S. / Welin, M. / Nyman, T. / Hammarstrom, M. / Moche, M. / Graslund, S. / Nordlund, P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j8q.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j8q.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 2j8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j8q ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j8q | HTTPS FTP |
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-Related structure data
Related structure data | 2cl3SC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9945, 0.02949, -0.1006), Vector: |
-Components
#1: Protein | Mass: 26420.318 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43809 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT HAS AN N-TERMINAL HIS TAG | |
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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: 2.72 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Details: 17%(W/V)PEG3350, 0.2M AMSO4, 0.1M BIS TRIS PH 5.2.MIX 1:1UL DROPS OF 9MG/ML PROTEIN WITH WELL SOLUTION IN RT THEN MOVE TO CR. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 24012 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.94 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CL3 Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.452 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.244 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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