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Yorodumi- PDB-7m0y: Crystal structure of the BRAF:MEK1 kinases in complex with AMPPNP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m0y | ||||||||||||
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Title | Crystal structure of the BRAF:MEK1 kinases in complex with AMPPNP and Trametinib | ||||||||||||
Components |
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Keywords | TRANSFERASE / BRAF / MEK1 | ||||||||||||
Function / homology | Function and homology information epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / placenta blood vessel development / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / regulation of axon regeneration / mitogen-activated protein kinase kinase / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / placenta blood vessel development / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / regulation of axon regeneration / mitogen-activated protein kinase kinase / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / head morphogenesis / Signalling to p38 via RIT and RIN / cerebellar cortex formation / 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 / Signaling by MAP2K mutants / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / regulation of Golgi inheritance / trachea formation / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / protein kinase activator activity / ERBB2-ERBB3 signaling pathway / stress fiber assembly / positive regulation of axon regeneration / face development / endodermal cell differentiation / MAPK3 (ERK1) activation / synaptic vesicle exocytosis / somatic stem cell population maintenance / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / MAP kinase kinase kinase activity / Schwann cell development / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / keratinocyte differentiation / positive regulation of stress fiber assembly / response to cAMP / ERK1 and ERK2 cascade / myelination / cellular response to calcium ion / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / long-term synaptic potentiation / cell motility / 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 / positive regulation of protein serine/threonine kinase activity / response to peptide hormone / neuron differentiation / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / cellular response to xenobiotic stimulus / late endosome / presynapse / cell body / positive regulation of peptidyl-serine phosphorylation / T cell differentiation in thymus / regulation of cell population proliferation / heart development / T cell receptor signaling pathway / scaffold protein binding / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / early endosome / non-specific serine/threonine protein kinase Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å | ||||||||||||
Authors | Li, K. / Gonzalez Del-Pino, G. / Ha, B.H. / Park, E. / Eck, M.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Allosteric MEK inhibitors act on BRAF/MEK complexes to block MEK activation. Authors: Gonzalez-Del Pino, G.L. / Li, K. / Park, E. / Schmoker, A.M. / Ha, B.H. / 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 | 7m0y.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m0y.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 7m0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/7m0y ftp://data.pdbj.org/pub/pdb/validation_reports/m0/7m0y | HTTPS FTP |
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-Related structure data
Related structure data | 6v2wC 7m0tC 7m0uC 7m0vC 7m0wC 7m0xC 7m0zC 6pp9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32098.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Plasmid: PFASTBAC DUAL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P15056, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 43790.281 Da / Num. of mol.: 1 / Mutation: S218A, S222A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Plasmid: pAC8 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q02750, mitogen-activated protein kinase kinase |
-Non-polymers , 4 types, 6 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-QOM / | |
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-Details
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: 3.35 Å3/Da / Density % sol: 67.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris 8.5, 200 mM Lithium Sulfate and 22% PEG 3,350 |
-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: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→47.08 Å / Num. obs: 13509 / % possible obs: 97.53 % / Redundancy: 4.8 % / Biso Wilson estimate: 86.09 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1498 / Rpim(I) all: 0.0755 / Rrim(I) all: 0.1685 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.451→3.575 Å / Rmerge(I) obs: 0.6754 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 1329 / CC1/2: 0.748 / Rpim(I) all: 0.3383 / Rrim(I) all: 0.758 / % possible all: 98.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PP9 Resolution: 3.45→47.08 Å / SU ML: 0.2753 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1489 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 77.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.45→47.08 Å
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Refine LS restraints |
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LS refinement shell |
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