+Open data
-Basic information
Entry | Database: PDB / ID: 5c0v | ||||||
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Title | Structure of the LARP1-unique domain DM15 | ||||||
Components | La-related protein 1 | ||||||
Keywords | RNA BINDING PROTEIN / RNA-binding / Heat-like / mRNA / helical repeat | ||||||
Function / homology | Function and homology information cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / TORC1 signaling / response to amino acid starvation / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / positive regulation of macroautophagy ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / TORC1 signaling / response to amino acid starvation / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / positive regulation of macroautophagy / ribosomal small subunit binding / TOR signaling / positive regulation of translational initiation / positive regulation of viral genome replication / negative regulation of translational initiation / translation initiation factor binding / mRNA 3'-UTR binding / positive regulation of translation / translational initiation / mRNA 5'-UTR binding / cytoplasmic stress granule / cell population proliferation / negative regulation of translation / cadherin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å | ||||||
Authors | Lahr, R.M. / Berman, A.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence. Authors: Lahr, R.M. / Mack, S.M. / Heroux, A. / Blagden, S.P. / Bousquet-Antonelli, C. / Deragon, J.M. / Berman, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c0v.cif.gz | 264.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c0v.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 5c0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c0v_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 5c0v_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 5c0v_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 5c0v_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/5c0v ftp://data.pdbj.org/pub/pdb/validation_reports/c0/5c0v | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | monomer by gel filtration |
-Components
#1: Protein | Mass: 19756.967 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PKG0 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.2 M Ammonium nitrate, 20% PEG 3350 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.976 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35696 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.25 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.2→42.567 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.567 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.0837 Å / Origin y: -3.4879 Å / Origin z: -47.9555 Å
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Refinement TLS group | Selection details: all |