+Open data
-Basic information
Entry | Database: PDB / ID: 6u2g | ||||||
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Title | BRAF-MEK complex with AMP-PCP bound to BRAF | ||||||
Components |
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Keywords | TRANSFERASE / Kinase / AMP-PCP / dimer / SIGNALING PROTEI | ||||||
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 / molecular replacement / Resolution: 2.886 Å | ||||||
Authors | Liau, N.P.D. / Wendorff, T. / Hymowitz, S. / Sudhamsu, J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2020 Title: Negative regulation of RAF kinase activity by ATP is overcome by 14-3-3-induced dimerization. Authors: Liau, N.P.D. / Wendorff, T.J. / Quinn, J.G. / Steffek, M. / Phung, W. / Liu, P. / Tang, J. / Irudayanathan, F.J. / Izadi, S. / Shaw, A.S. / Malek, S. / Hymowitz, S.G. / Sudhamsu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u2g.cif.gz | 255.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u2g.ent.gz | 202.5 KB | Display | PDB format |
PDBx/mmJSON format | 6u2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/6u2g ftp://data.pdbj.org/pub/pdb/validation_reports/u2/6u2g | HTTPS FTP |
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-Related structure data
Related structure data | 6u2hC 4mneS 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: 43506.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q02750, mitogen-activated protein kinase kinase |
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#2: Protein | Mass: 35217.633 Da / Num. of mol.: 1 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 |
-Non-polymers , 4 types, 38 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.29 Å3/Da / Density % sol: 62.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate, MES, PEK 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.886→80.159 Å / Num. obs: 23613 / % possible obs: 99.05 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.02315 / Net I/av σ(I): 17.85 / Net I/σ(I): 17.85 |
Reflection shell | Resolution: 2.886→2.989 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 2337 / CC1/2: 0.786 / % possible all: 99.96 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MNE Resolution: 2.886→80.159 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.48 / 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: 194.95 Å2 / Biso mean: 79.0371 Å2 / Biso min: 37.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.886→80.159 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 52.4199 Å / Origin y: -44.4515 Å / Origin z: -17.9216 Å
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Refinement TLS group |
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