+Open data
-Basic information
Entry | Database: PDB / ID: 6gd1 | ||||||
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Title | Structure of HuR RRM3 | ||||||
Components | Thioredoxin 1,ELAV-like protein 1 | ||||||
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 / DNA polymerase processivity factor activity ...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 / DNA polymerase processivity factor activity / mRNA destabilization / sarcoplasm / protein-disulfide reductase activity / positive regulation of superoxide anion generation / cell redox homeostasis / 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 | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 | 6gd1.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gd1.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gd1_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 6gd1_full_validation.pdf.gz | 439.3 KB | Display | |
Data in XML | 6gd1_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 6gd1_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/6gd1 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/6gd1 | HTTPS FTP |
-Related structure data
Related structure data | 6g2kC 6gd2C 6gd3C 2trxS 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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Unit cell |
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-Components
#1: Protein | Mass: 22775.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human) Strain: K12 / Gene: trxA, fipA, tsnC, b3781, JW5856, ELAVL1, HUR / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25, UniProt: Q15717 #2: Chemical | ChemComp-NA / #3: 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: 2.24 Å3/Da / Density % sol: 44.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23% (w/v) PEG 2000 MME, 0.1 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.042 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.042 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→8.99 Å / Num. obs: 26790 / % possible obs: 99.7 % / Redundancy: 6.73 % / Rrim(I) all: 0.1 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 2.01→2.06 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1988 / Rrim(I) all: 0.85 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2TRX Resolution: 2.01→8.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.878 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.179 / 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: 39.844 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→8.98 Å
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Refine LS restraints |
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