[English] 日本語
Yorodumi- PDB-1kl9: Crystal structure of the N-terminal segment of Human eukaryotic i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kl9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal segment of Human eukaryotic initiation factor 2alpha | ||||||
Components | EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 | ||||||
Keywords | TRANSLATION / OB FOLD / HELICAL DOMAIN | ||||||
Function / homology | Function and homology information regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / Cellular response to mitochondrial stress / glial limiting end-foot / response to kainic acid / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP ...regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / Cellular response to mitochondrial stress / glial limiting end-foot / response to kainic acid / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / eukaryotic translation initiation factor 2 complex / PERK regulates gene expression / regulation of translational initiation in response to stress / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / stress granule assembly / translational initiation / cellular response to amino acid starvation / translation initiation factor activity / response to endoplasmic reticulum stress / ABC-family proteins mediated transport / PKR-mediated signaling / cytoplasmic stress granule / cellular response to UV / ribosome binding / cellular response to heat / cellular response to oxidative stress / synapse / RNA binding / extracellular exosome / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Nonato, M.C. / Widom, J. / Clardy, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of the N-terminal segment of human eukaryotic translation initiation factor 2alpha Authors: Nonato, M.C. / Widom, J. / Clardy, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kl9.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kl9.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/1kl9 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/1kl9 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
3 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21439.061 Da / Num. of mol.: 1 / Fragment: residues 1-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05198 | ||
---|---|---|---|
#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 4000, sodium acetate, zinc chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP at 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795, 0.9793, 0.9640 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 27, 2000 | ||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.9→60 Å / Num. obs: 14922 / % possible obs: 90.9 % / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.7 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 3 / % reflection Rfree: 4.9 % / Rfactor all: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|