+Open data
-Basic information
Entry | Database: PDB / ID: 7shv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of BRAF kinase domain bound to GDC0879 | ||||||
Components | Serine/threonine-protein kinase B-raf | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / kinase / kinase inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | Function and homology information trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / head morphogenesis / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / head morphogenesis / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / positive regulation of axonogenesis / Frs2-mediated activation / stress fiber assembly / positive regulation of axon regeneration / face development / synaptic vesicle exocytosis / somatic stem cell population maintenance / MAP kinase kinase activity / thyroid gland development / MAP kinase kinase kinase activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / response to cAMP / ERK1 and ERK2 cascade / cellular response to calcium ion / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / thymus development / long-term synaptic potentiation / animal organ morphogenesis / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / visual learning / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / response to peptide hormone / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / cellular response to xenobiotic stimulus / presynapse / cell body / positive regulation of peptidyl-serine phosphorylation / T cell differentiation in thymus / regulation of cell population proliferation / T cell receptor signaling pathway / scaffold protein binding / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / protein phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Kung, J.E. / Sudhamsu, J. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: Clearing the Path to Rapid High-Quality Protein Purification Authors: Chen, X. / Wendorff, T. / Jao, C. / Kung, J.E. / Liau, N.P.D. / Wu, P. / Yu, C. / Oh, A. / Boenig, G. / Wallweber, H. / Everett, C. / Miu, A. / Brillantes, B. / Mortara, K. / Murray, J. / ...Authors: Chen, X. / Wendorff, T. / Jao, C. / Kung, J.E. / Liau, N.P.D. / Wu, P. / Yu, C. / Oh, A. / Boenig, G. / Wallweber, H. / Everett, C. / Miu, A. / Brillantes, B. / Mortara, K. / Murray, J. / Koth, C.M. / Sudhamsu, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7shv.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7shv.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 7shv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/7shv ftp://data.pdbj.org/pub/pdb/validation_reports/sh/7shv | HTTPS FTP |
---|
-Related structure data
Related structure data | 7si1C 4mnfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35330.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P15056, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: 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: 2.8 Å3/Da / Density % sol: 56.1 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 5.5 Details: 0.1 M Na Cacodylate pH 5.5, 0.1 M Ca Acetate, 12% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→39.78 Å / Num. obs: 18435 / % possible obs: 94 % / Redundancy: 13.3 % / Biso Wilson estimate: 74.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.07641 / Rrim(I) all: 0.2805 / Rsym value: 0.2696 / Net I/σ(I): 10.23 |
Reflection shell | Resolution: 2.88→3.065 Å / Redundancy: 14.1 % / Num. unique obs: 1795 / CC1/2: 0.721 / CC star: 0.915 / % possible all: 85.12 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MNF Resolution: 2.88→39.78 Å / SU ML: 0.4693 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2432 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.64 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→39.78 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|