+Open data
-Basic information
Entry | Database: PDB / ID: 7osy | ||||||||||||
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Title | Human Prolyl-tRNA Synthetase in Complex with L-proline | ||||||||||||
Components | Bifunctional glutamate/proline--tRNA ligase | ||||||||||||
Keywords | LIGASE / beta barrel / tRNA synthetase / protein-ligand complex | ||||||||||||
Function / homology | Function and homology information regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / RNA stem-loop binding / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||||||||
Authors | Pang, L. / Zitko, J. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies. Authors: Pang, L. / Weeks, S.D. / Juhas, M. / Strelkov, S.V. / Zitko, J. / Van Aerschot, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7osy.cif.gz | 396.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7osy.ent.gz | 321.2 KB | Display | PDB format |
PDBx/mmJSON format | 7osy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/7osy ftp://data.pdbj.org/pub/pdb/validation_reports/os/7osy | HTTPS FTP |
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-Related structure data
Related structure data | 7oszC 7ot0C 7ot1C 7ot2C 7ot3C 5vadS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 58087.375 Da / Num. of mol.: 2 / Fragment: Prolyl-tRNA synthetase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SR / #5: 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: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a ...Details: The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a Terasaki Microbatch plate by mixing 1 uL the pre-mix with 1 uL of reservoir solution containing 0.25-0.4 M SrCl2, 15-20% (v/v) PEG3350 and 100 mM HEPES pH 7.5. The drops were covered with paraffin oil. Crystals were flash frozen in liquid nitrogen directly from the plate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→78.59 Å / Num. obs: 47590 / % possible obs: 98.3 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.037 / Rrim(I) all: 0.082 / Net I/σ(I): 11.3 / Num. measured all: 226553 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.3
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VAD Resolution: 2.23→44.2 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.96 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 190 Å2 / Biso mean: 63.5721 Å2 / Biso min: 24.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→44.2 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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