+Open data
-Basic information
Entry | Database: PDB / ID: 6nyb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a MAPK pathway complex | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / CD4-positive, alpha-beta T cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / labyrinthine layer development / MAP-kinase scaffold activity ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / CD4-positive, alpha-beta T cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / labyrinthine layer development / MAP-kinase scaffold activity / type B pancreatic cell proliferation / Signalling to p38 via RIT and RIN / cerebellar cortex formation / head morphogenesis / 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 / spindle pole body / MAP kinase kinase kinase activity / mitogen-activated protein kinase kinase binding / trachea formation / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / positive regulation of axonogenesis / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / stress fiber assembly / protein kinase activator activity / positive regulation of axon regeneration / endodermal cell differentiation / MAPK3 (ERK1) activation / face development / synaptic vesicle exocytosis / somatic stem cell population maintenance / MAP kinase kinase activity / Bergmann glial cell differentiation / thyroid gland development / Uptake and function of anthrax toxins / negative regulation of endothelial cell apoptotic process / Schwann cell development / positive regulation of substrate adhesion-dependent cell spreading / keratinocyte differentiation / Signal transduction by L1 / positive regulation of stress fiber assembly / response to cAMP / cellular response to calcium ion / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / myelination / substrate adhesion-dependent cell spreading / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / insulin-like growth factor receptor signaling pathway / cellular response to nerve growth factor stimulus / thymus development / epidermal growth factor receptor signaling pathway / cell motility / long-term synaptic potentiation / animal organ morphogenesis / RAF activation / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / positive regulation of protein serine/threonine kinase activity / cellular senescence / neuron differentiation / response to peptide hormone / cellular response to xenobiotic stimulus / 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 / positive regulation of peptidyl-serine phosphorylation / MAPK cascade / Signaling by BRAF and RAF1 fusions / late endosome / presynapse / heart development / T cell receptor signaling pathway / regulation of cell population proliferation / protein tyrosine kinase activity / cell body / T cell differentiation in thymus / scaffold protein binding / 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) Spodoptera exigua (beet armyworm) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Park, E. / Rawson, S. / Li, K. / Jeon, H. / Eck, M.J. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nature / Year: 2019 Title: Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes. Authors: Eunyoung Park / Shaun Rawson / Kunhua Li / Byeong-Won Kim / Scott B Ficarro / Gonzalo Gonzalez-Del Pino / Humayun Sharif / Jarrod A Marto / Hyesung Jeon / Michael J Eck / Abstract: RAF family kinases are RAS-activated switches that initiate signalling through the MAP kinase cascade to control cellular proliferation, differentiation and survival. RAF activity is tightly ...RAF family kinases are RAS-activated switches that initiate signalling through the MAP kinase cascade to control cellular proliferation, differentiation and survival. RAF activity is tightly regulated and inappropriate activation is a frequent cause of cancer; however, the structural basis for RAF regulation is poorly understood at present. Here we use cryo-electron microscopy to determine autoinhibited and active-state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer. The reconstruction reveals an inactive BRAF-MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding cysteine-rich domain and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, which drives the formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nyb.cif.gz | 218 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6nyb.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nyb_validation.pdf.gz | 983.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6nyb_full_validation.pdf.gz | 992.9 KB | Display | |
Data in XML | 6nyb_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 6nyb_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/6nyb ftp://data.pdbj.org/pub/pdb/validation_reports/ny/6nyb | HTTPS FTP |
-Related structure data
Related structure data | 0541MC 6pp9C 6q0jC 6q0kC 6q0tC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 3 types, 4 molecules ABCD
#1: Protein | Mass: 89402.789 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 |
---|---|
#2: Protein | Mass: 45934.543 Da / Num. of mol.: 1 / Mutation: S218A, S222A Source method: isolated from a genetically manipulated source Details: GDC-0623 / Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q02750, mitogen-activated protein kinase kinase |
#3: Protein | Mass: 28108.514 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spodoptera exigua (beet armyworm) / References: UniProt: V9P4T4 |
-Non-polymers , 5 types, 6 molecules
#4: Chemical | ChemComp-AGS / | ||||||
---|---|---|---|---|---|---|---|
#5: Chemical | #6: Chemical | ChemComp-ADP / | #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-LCJ / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of BRAF/MEK1/14-3-3 with MEK inhibitor Type: COMPLEX Details: 14-3-3 is heterodimer of Insect epsilon and zeta. model was generated by Insect zeta sequence as a homo-dimer. Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 0.19 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165298 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|