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Yorodumi- PDB-8rzv: Structure of UP1 S4ES6E phosphomimetic mutant in complex with hum... -
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-Basic information
Entry | Database: PDB / ID: 8rzv | ||||||
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Title | Structure of UP1 S4ES6E phosphomimetic mutant in complex with human telomeric repeat DNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / hnRNP A1 / RNA/DNA BINDING PROTEIN / RNA-DNA BINDING PROTEIN-DNA complex / RRM | ||||||
Function / homology | Function and homology information cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / localization / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Dunnett, L. / Prischi, F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of UP1 S4ES6E phosphomimetic mutant in complex with human telomeric repeat DNA Authors: Dunnett, L. / Prischi, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rzv.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rzv.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 8rzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/8rzv ftp://data.pdbj.org/pub/pdb/validation_reports/rz/8rzv | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22441.182 Da / Num. of mol.: 1 / Mutation: S4E, S6E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Plasmid: pETM-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09651 |
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#2: DNA chain | Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.50, 1.7 M Ammonium Phosphate Dibasic, 15 % (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→44.03 Å / Num. obs: 36927 / % possible obs: 99.24 % / Redundancy: 2 % / Biso Wilson estimate: 21.97 Å2 / CC1/2: 1 / Rrim(I) all: 0.084 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3543 / CC1/2: 0.7 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→44.03 Å / SU ML: 0.1904 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2214 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→44.03 Å
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Refine LS restraints |
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LS refinement shell |
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