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- PDB-1zyd: Crystal Structure of eIF2alpha Protein Kinase GCN2: Wild-Type Com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zyd | ||||||
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Title | Crystal Structure of eIF2alpha Protein Kinase GCN2: Wild-Type Complexed with ATP. | ||||||
![]() | Serine/threonine-protein kinase GCN2 | ||||||
![]() | TRANSFERASE / TRANSLATION REGULATOR / PROTEIN KINASE / SIGNAL TRANSDUCTION / AMINO-ACID STARVATION / STARVATION STRESS RESPONSE / EIF2ALPHA KINASE | ||||||
Function / homology | ![]() cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding ...cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding / cytosolic ribosome / translation initiation factor binding / cellular response to amino acid starvation / DNA damage checkpoint signaling / large ribosomal subunit / : / double-stranded RNA binding / ribosome binding / small ribosomal subunit / protein autophosphorylation / tRNA binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / translation / protein phosphorylation / protein serine kinase activity / protein homodimerization activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Padyana, A.K. / Qiu, H. / Roll-Mecak, A. / Hinnebusch, A.G. / Burley, S.K. | ||||||
![]() | ![]() Title: Structural Basis for Autoinhibition and Mutational Activation of Eukaryotic Initiation Factor 2{alpha} Protein Kinase GCN2 Authors: Padyana, A.K. / Qiu, H. / Roll-Mecak, A. / Hinnebusch, A.G. / Burley, S.K. | ||||||
History |
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Remark 600 | HETEROGEN ATP 303, MG 305, and MG 306 are associated with protein chain A ATP 304, MG 307, and MG ...HETEROGEN ATP 303, MG 305, and MG 306 are associated with protein chain A ATP 304, MG 307, and MG 308 are associated with protein chain B |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.9 KB | Display | ![]() |
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PDB format | ![]() | 96.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zxeSC ![]() 1zy4C ![]() 1zy5C ![]() 1zycC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly of GCN2 protein kinase is a dimer. The asymmetric unit of this crystal lattice contains one dimer assembled into one biological unit. |
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Components
#1: Protein | Mass: 35143.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GCN2, AAS1 / Plasmid: pET26b / Production host: ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 Details: PEG 3350, CHES, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 11, 2004 |
Radiation | Monochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 18487 / Num. obs: 18366 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.75→2.81 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZXE Resolution: 2.75→47.59 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1390079.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9052 Å2 / ksol: 0.35526 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→47.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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