+Open data
-Basic information
Entry | Database: PDB / ID: 6gd3 | ||||||
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Title | Structure of HuR RRM3 in complex with RNA (UAUUUA) | ||||||
Components |
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Keywords | RNA BINDING PROTEIN | ||||||
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 / mRNA 3'-UTR binding / positive regulation of translation / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Pabis, M. / Sattler, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs. Authors: Pabis, M. / Popowicz, G.M. / Stehle, R. / Fernandez-Ramos, D. / Asami, S. / Warner, L. / Garcia-Maurino, S.M. / Schlundt, A. / Martinez-Chantar, M.L. / Diaz-Moreno, I. / Sattler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gd3.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gd3.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gd3_validation.pdf.gz | 471.8 KB | Display | wwPDB validaton report |
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Full document | 6gd3_full_validation.pdf.gz | 476.2 KB | Display | |
Data in XML | 6gd3_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6gd3_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/6gd3 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/6gd3 | HTTPS FTP |
-Related structure data
Related structure data | 6g2kC 6gd1SC 6gd2C 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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Unit cell |
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-Components
#1: Protein | Mass: 9701.152 Da / Num. of mol.: 3 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 #2: RNA chain | | Mass: 1838.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-NA / | #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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 0.01 M calcium chloride, 0.05 M sodium cacodylate pH 6.5 and 10 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.007 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→6.04 Å / Num. obs: 62913 / % possible obs: 98.7 % / Redundancy: 3.36 % / Rrim(I) all: 0.072 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 1.35→1.39 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 4560 / Rrim(I) all: 0.67 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GD1 Resolution: 1.35→6.04 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.932 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.053 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.115 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→6.04 Å
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Refine LS restraints |
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