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Yorodumi- PDB-5kwq: Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kwq | ||||||
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Title | Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also Known as PUF60 | ||||||
Components | Poly(U)-binding-splicing factor PUF60 | ||||||
Keywords | SPLICING / Tandem RRMs / c-Myc Regulation / Splicing Factor | ||||||
Function / homology | Function and homology information alternative mRNA splicing, via spliceosome / mRNA splice site recognition / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / apoptotic process / DNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Crichlow, G.V. / Yang, Y. / Zhou, H. / Lolis, E.J. / Braddock, D.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos One / Year: 2020 Title: Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60. Authors: Hsiao, H.T. / Crichlow, G.V. / Murphy, J.W. / Folta-Stogniew, E.J. / Lolis, E.J. / Braddock, D.T. #1: Journal: EMBO J. / Year: 2008 Title: Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition. Authors: Crichlow, G.V. / Zhou, H. / Hsiao, H.H. / Frederick, K.B. / Debrosse, M. / Yang, Y. / Folta-Stogniew, E.J. / Chung, H.J. / Fan, C. / De la Cruz, E.M. / Levens, D. / Lolis, E. / Braddock, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kwq.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kwq.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kwq_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 5kwq_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 5kwq_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5kwq_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/5kwq ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kwq | HTTPS FTP |
-Related structure data
Related structure data | 5kvyC 5kw1C 5kw6C 2qfjS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23408.537 Da / Num. of mol.: 2 / Mutation: R106G, C112S, C238A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PUF60, FIR, ROBPI, SIAHBP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UHX1 |
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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: 1.89 Å3/Da / Density % sol: 34.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1M Lithium sulfate, 0.1M HEPES (pH 7.5), 5% glycerol, mixed with an equal volume of 10 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 13, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 11918 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 110.2 Å2 / Rmerge(I) obs: 0.071 / Net I/av σ(I): 12.7 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.745 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QFJ Resolution: 2.8→19.63 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1594738.79 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 36.3683 Å2 / ksol: 0.34409 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.4 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2.8→19.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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