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Yorodumi- PDB-4egl: Crystal structure of two tandem RNA recognition motifs of Human a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4egl | ||||||
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Title | Crystal structure of two tandem RNA recognition motifs of Human antigen R | ||||||
Components | ELAV-like protein 1 | ||||||
Keywords | RNA BINDING PROTEIN / RRM / RNA Binding / Cytoplasm and Nucleus | ||||||
Function / homology | Function and homology information HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization ...HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA destabilization / sarcoplasm / positive regulation of superoxide anion generation / positive regulation of translation / mRNA 3'-UTR binding / P-body / protein homooligomerization / cytoplasmic stress granule / protein import into nucleus / double-stranded RNA binding / cytoplasmic vesicle / postsynapse / ribonucleoprotein complex / mRNA binding / glutamatergic synapse / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wang, H. / Zeng, F. / Liu, H. / Teng, M. / Li, X. | ||||||
Citation | Journal: To be Published Title: Crystal structure of two tandem RNA recognition motifs of Human antigen R Authors: Wang, H. / Zeng, F. / Liu, H. / Teng, M. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4egl.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4egl.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4egl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/4egl ftp://data.pdbj.org/pub/pdb/validation_reports/eg/4egl | HTTPS FTP |
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-Related structure data
Related structure data | 1fxlS 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: 19839.420 Da / Num. of mol.: 1 Fragment: N-terminal RRM1 and RRM2 domain, UNP residues 18-186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELAVL1, HUR / Production host: Escherichia coli (E. coli) / References: UniProt: Q15717 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.58 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5M Lithium sulfate monohydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.99985 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 21, 2010 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 4179 / Num. obs: 4062 / % possible obs: 97.3 % |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.26 / Rsym value: 0.366 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FXL Resolution: 2.9→39.33 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.854 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 52.296 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / 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: 59.645 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→39.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.896→2.971 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -4.8111 Å / Origin y: 15.3323 Å / Origin z: -2.3802 Å
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