[English] 日本語
Yorodumi- PDB-6iy6: Crystal structure of human cytosolic aspartyl-tRNA synthetase (DR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iy6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS) | |||||||||
Components |
| |||||||||
Keywords | TRANSLATION / Aminoacyl-tRNA transferase Glutathion-S transferase domain | |||||||||
Function / homology | Function and homology information type II pneumocyte differentiation / aspartate-tRNA ligase / aminoacylase activity / aspartyl-tRNA aminoacylation / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase ...type II pneumocyte differentiation / aspartate-tRNA ligase / aminoacylase activity / aspartyl-tRNA aminoacylation / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of protein ubiquitination / cellular response to insulin stimulus / cellular response to type II interferon / RNA stem-loop binding / GTPase binding / protein-containing complex assembly / molecular adaptor activity / negative regulation of translation / protein ubiquitination / translation / ribonucleoprotein complex / negative regulation of cell population proliferation / synapse / apoptotic process / protein homodimerization activity / RNA binding / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Park, S.H. / Hahn, H. / Han, B.W. | |||||||||
Funding support | Korea, Republic Of, 2items
| |||||||||
Citation | Journal: Iucrj / Year: 2019 Title: The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex. Authors: Hahn, H. / Park, S.H. / Kim, H.J. / Kim, S. / Han, B.W. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6iy6.cif.gz | 610.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iy6.ent.gz | 499 KB | Display | PDB format |
PDBx/mmJSON format | 6iy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iy6_validation.pdf.gz | 557.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6iy6_full_validation.pdf.gz | 581.8 KB | Display | |
Data in XML | 6iy6_validation.xml.gz | 98.8 KB | Display | |
Data in CIF | 6iy6_validation.cif.gz | 132.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iy6 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iy6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 12 molecules ABGHCDIJEFKL
#1: Protein | Mass: 57310.121 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DARS, PIG40 / Production host: Escherichia coli (E. coli) / References: UniProt: P14868, aspartate-tRNA ligase #2: Protein | Mass: 24165.006 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13155 #3: Protein | Mass: 18434.824 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli) References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase |
---|
-Non-polymers , 3 types, 31 molecules
#4: Chemical | #5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.5 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M CAPS (pH 10.5) 1.3 M sodium phosphate monobasic 0.5 M potassium phosphate dibasic 0.5 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 61327 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rsym value: 0.103 / Net I/σ(I): 8.18 |
Reflection shell | Resolution: 3.6→3.66 Å / Num. unique obs: 2998 / Rsym value: 0.772 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J15, 5A34 Resolution: 3.6→30 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→30 Å
| ||||||||||||||||
LS refinement shell | Resolution: 3.6→3.7286 Å
|