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Yorodumi- PDB-6v34: Crystal structure of BRAF V600E oncogenic mutant in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 6v34 | |||||||||
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Title | Crystal structure of BRAF V600E oncogenic mutant in complex with TAK-580 | |||||||||
Components | Serine/threonine-protein kinase B-raf | |||||||||
Keywords | TRANSFERASE / BRAF | |||||||||
Function / homology | Function and homology information small GTPase binding => GO:0031267 / cellular response to xenobiotic stimulus => GO:0071466 / protein serine/threonine kinase activity => GO:0004674 / 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 ...small GTPase binding => GO:0031267 / cellular response to xenobiotic stimulus => GO:0071466 / protein serine/threonine kinase activity => GO:0004674 / 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: 3.15 Å | |||||||||
Authors | Gonzalez Del-Pino, G. / Li, K. / Eck, M.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Crystal structure of BRAF V600E oncogenic mutant in complex with TAK-580 Authors: Gonzalez Del-Pino, G. / Li, K. / Eck, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v34.cif.gz | 222.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v34.ent.gz | 177.7 KB | Display | PDB format |
PDBx/mmJSON format | 6v34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/6v34 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v34 | HTTPS FTP |
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-Related structure data
Related structure data | 5itaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32044.666 Da / Num. of mol.: 2 Mutation: I543A, I544S, I551K, Q562R, L588N, K630S, F667E, Y673S, A688R, L706S, Q709R, S713E, L716E, S720E, P722S, K723A, V600E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: A0A2R8Y8E0, UniProt: P15056*PLUS #2: Chemical | Has ligand of interest | Y | |
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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: 1.99 Å3/Da / Density % sol: 38.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Sodium Acetate, 0.1 M Tris: HCl, pH 8.5, 30 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→24.925 Å / Num. obs: 9189 / % possible obs: 96.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 73.37 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.2515 / Rpim(I) all: 0.1126 / Rrim(I) all: 0.2675 / Net I/σ(I): 7.56 |
Reflection shell | Resolution: 3.15→3.263 Å / Mean I/σ(I) obs: 1.55 / Num. unique obs: 893 / CC1/2: 0.708 / Rpim(I) all: 0.6916 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ITA Resolution: 3.15→24.92 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.39 Å2 / Biso mean: 81.5009 Å2 / Biso min: 42.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.15→24.92 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 2.9358 Å / Origin y: -13.9754 Å / Origin z: 27.1289 Å
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Refinement TLS group |
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