+Open data
-Basic information
Entry | Database: PDB / ID: 4zc4 | ||||||
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Title | Crystal structure of 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 / translational initiation / translation initiation factor binding / mRNA 3'-UTR binding / positive regulation of translation / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 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. #1: Journal: To Be Published Title: The LARP1-specific domain DM15 repurposes HEAT-like repeats to directly bind messenger RNA 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 | 4zc4.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zc4.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 4zc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/4zc4 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zc4 | HTTPS FTP |
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-Related 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: 19616.281 Da / Num. of mol.: 4 / Fragment: UNP residues 873-1023 Source method: isolated from a genetically manipulated source Details: QHPSHELLKENGFTQHVYHKYRRRCLNERKRLGIGQSQEMNTLFRFWSFFLRDHFNKKMYEEFKQLALEDAKEGYRYGLECLFRYYSYGLEKKFRLDIFKDFQEETVKDYEAGQLYGLEKFWAFLKYSKAKNLDIDPKLQEYLGKFR Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 304 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.225 M ammonium chloride, pH 6.3, 23% PEG 3350 / Temp details: Room Temp |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→76.57 Å / Num. obs: 87993 / % possible obs: 95 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 34.582 |
Reflection shell | Highest resolution: 1.62 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 1.4 / % possible all: 63.66 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.86→38.285 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.54 / 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: 1.86→38.285 Å
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Refine LS restraints |
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LS refinement shell |
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