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Yorodumi- PDB-6pw3: LARP1 DM15 FYRE (F844Y, R847E) mutant bound to m7GpppG dinucleoti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pw3 | |||||||||
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Title | LARP1 DM15 FYRE (F844Y, R847E) mutant bound to m7GpppG dinucleotide (capG) | |||||||||
Components | La-related protein 1 | |||||||||
Keywords | RNA BINDING PROTEIN / HEAT-like / cap-binding / TOP mRNA / translation regulation | |||||||||
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 / translational initiation / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Lahr, R.M. / Berman, A.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2019 Title: Capturing the Mechanism Underlying TOP mRNA Binding to LARP1. Authors: Cassidy, K.C. / Lahr, R.M. / Kaminsky, J.C. / Mack, S. / Fonseca, B.D. / Das, S.R. / Berman, A.J. / Durrant, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pw3.cif.gz | 295 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pw3.ent.gz | 195.2 KB | Display | PDB format |
PDBx/mmJSON format | 6pw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pw3_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 6pw3_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 6pw3_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 6pw3_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/6pw3 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/6pw3 | HTTPS FTP |
-Related structure data
Related structure data | 4zc4S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19604.201 Da / Num. of mol.: 4 / Mutation: F844Y, R847E 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: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 100 mM Hepes 7.5, 0.08 M NaCl, 36% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→29.3 Å / Num. obs: 30894 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 54.3315929648 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.34→2.4 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 2210 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZC4 Resolution: 2.34→29.24 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→29.24 Å
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Refine LS restraints |
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LS refinement shell |
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