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Yorodumi- PDB-5kvy: CRYSTAL STRUCTURE OF THE TWO TANDEM RRM DOMAINS OF PUF60 BOUND TO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kvy | |||||||||
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Title | CRYSTAL STRUCTURE OF THE TWO TANDEM RRM DOMAINS OF PUF60 BOUND TO A PORTION OF AN ADML PRE-MRNA 3' SPLICE SITE ANALOG | |||||||||
Components |
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Keywords | SPLICING/DNA / TANDEM RRMS / PROTEIN-NUCLEIC ACID COMPLEX / SPLICING FACTOR / SPLICING-DNA complex | |||||||||
Function / homology | Function and homology information alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | |||||||||
Model details | protein / nucleic acid complex | |||||||||
Authors | Hsiao, H.-H. / Crichlow, G.V. / Albright, R.A. / Murphy, J.W. / 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 | 5kvy.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kvy.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/5kvy ftp://data.pdbj.org/pub/pdb/validation_reports/kv/5kvy | HTTPS FTP |
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-Related structure data
Related structure data | 5kw1C 5kw6C 5kwqC 2qfjS 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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Details | Authors have supported the biological unit analysis by performing size exclusion chromatography and light scattering |
-Components
#1: Protein | Mass: 23408.537 Da / Num. of mol.: 2 / Fragment: tandem RRM domains / Mutation: R123G, C129S, C255A 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 #2: DNA chain | | Mass: 8862.427 Da / Num. of mol.: 1 / Fragment: AdML3' / Source method: obtained synthetically Details: Sequence from the adenovirus major late pre-mRNA 3'splice site Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-CL / | #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: 1.68 Å3/Da / Density % sol: 26.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1 M TRIS-HCl, 25% PEG 4000, 5-10 mM Barium Chloride Dihydrate, pH 8.7, mixed with 10 mg/ml protein-nucleic acid mixture in 50 mM TRIS-HCl, pH 8.0, 150 mM NaCl, 20 micromolar EDTA. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 26419 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QFJ Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / Details: DATA WERE DE-TWINNED DURING REFINEMENT PROCESS
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Displacement parameters | Biso mean: 34.49 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å
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