+Open data
-Basic information
Entry | Database: PDB / ID: 8j9s | ||||||
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Title | leucine zipper complex of AIMP1 and AIMP2 | ||||||
Components |
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Keywords | TRANSLATION / aminoacyl-tRNA synthetase | ||||||
Function / homology | Function and homology information type II pneumocyte differentiation / positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / positive regulation of protein ubiquitination / cytokine activity / GTPase binding ...type II pneumocyte differentiation / positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / positive regulation of protein ubiquitination / cytokine activity / GTPase binding / cell-cell signaling / protein-containing complex assembly / angiogenesis / defense response to virus / tRNA binding / molecular adaptor activity / protein ubiquitination / inflammatory response / translation / negative regulation of cell population proliferation / apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Kim, D.K. / Kang, B.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Assembly of human multi-tRNA synthetase complex through leucine zipper motifs Authors: Kim, D.K. / Kang, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j9s.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j9s.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 8j9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/8j9s ftp://data.pdbj.org/pub/pdb/validation_reports/j9/8j9s | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Other experimental results indicate that AIMP1 interacts both AIMP1 and AIMP2 through its C-and N-terminal parts, respectively. |
-Components
#1: Protein | Mass: 9124.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12904 #2: Protein/peptide | | Mass: 5668.402 Da / Num. of mol.: 1 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: Chemical | ChemComp-IOD / Has ligand of interest | N | |
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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: 3.54 Å3/Da / Density % sol: 65.28 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 62% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 7226 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 1 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 3→3.05 Å / Num. unique obs: 346 / CC1/2: 0.785 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→34.66 Å / SU ML: 0.408 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 25.7525 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→34.66 Å
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Refine LS restraints |
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LS refinement shell |
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