[English] 日本語
Yorodumi- PDB-7qq6: GCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 1 (dovi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qq6 | ||||||
---|---|---|---|---|---|---|---|
Title | GCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 1 (dovitinib) | ||||||
Components | eIF-2-alpha kinase GCN2 | ||||||
Keywords | TRANSFERASE / EIF2 kinase / Integrated Stress Response / GCN2 | ||||||
Function / homology | Function and homology information positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / negative regulation of CREB transcription factor activity / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / negative regulation by host of viral genome replication / regulation of feeding behavior ...positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / negative regulation of CREB transcription factor activity / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / negative regulation by host of viral genome replication / regulation of feeding behavior / T cell activation involved in immune response / positive regulation of adaptive immune response / regulation of translational initiation / cellular response to cold / neuron projection extension / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of neuron differentiation / long-term memory / cytosolic ribosome / negative regulation of translational initiation / positive regulation of defense response to virus by host / cellular response to amino acid starvation / learning / DNA damage checkpoint signaling / positive regulation of long-term synaptic potentiation / cellular response to UV / defense response to virus / viral translation / adaptive immune response / protein autophosphorylation / tRNA binding / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Maia de Oliveira, T. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Biochem.J. / Year: 2020 Title: The structure of human GCN2 reveals a parallel, back-to-back kinase dimer with a plastic DFG activation loop motif. Authors: Maia de Oliveira, T. / Korboukh, V. / Caswell, S. / Winter Holt, J.J. / Lamb, M. / Hird, A.W. / Overman, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qq6.cif.gz | 231.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qq6.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qq6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qq6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7qq6_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 7qq6_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qq6 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qq6 | HTTPS FTP |
-Related structure data
Related structure data | 7qwkC 1zydS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 36784.641 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK4, GCN2, KIAA1338 / Production host: Escherichia coli (E. coli) References: UniProt: Q9P2K8, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-38O / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES pH6 with 20 per cent PEG 8000 and 200mM calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97857 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→49.36 Å / Num. obs: 38997 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 92 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.79→2.87 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.674 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 17912 / % possible all: 94.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZYD Resolution: 2.8→24.64 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.854 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.759 / SU Rfree Blow DPI: 0.331 / SU Rfree Cruickshank DPI: 0.341
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200.82 Å2 / Biso mean: 91.21 Å2 / Biso min: 45.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→24.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
|