+Open data
-Basic information
Entry | Database: PDB / ID: 8dgs | ||||||||||||
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Title | Cryo-EM structure of a RAS/RAF complex (state 1) | ||||||||||||
Components |
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Keywords | TRANSFERASE / kinase complex | ||||||||||||
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 / head morphogenesis / MAP-kinase scaffold activity / 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 / 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 / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / protein kinase activator activity / stress fiber assembly / positive regulation of axon regeneration / endodermal cell differentiation / face development / 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 / cellular response to calcium ion / myelination / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / substrate adhesion-dependent cell spreading / small monomeric GTPase / insulin-like growth factor receptor signaling pathway / cellular response to nerve growth factor stimulus / 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 / MAP2K and MAPK activation / visual learning / neuron differentiation / positive regulation of protein serine/threonine kinase activity / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / cellular response to xenobiotic stimulus / late endosome / presynapse / positive regulation of peptidyl-serine phosphorylation / T cell differentiation in thymus / cell body / heart development / regulation of cell population proliferation / T cell receptor signaling pathway / scaffold protein binding / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Spodoptera exigua (beet armyworm) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||
Authors | Eck, M.J. / Jeon, H. / Park, E. / Rawson, S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of a RAS/RAF recruitment complex. Authors: Eunyoung Park / Shaun Rawson / Anna Schmoker / Byeong-Won Kim / Sehee Oh / Kangkang Song / Hyesung Jeon / Michael J Eck / Abstract: RAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF ...RAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF have focused on the isolated RAS-binding and cysteine-rich domains of RAF (RBD and CRD, respectively), which interact directly with RAS. Here we describe cryo-EM structures of a KRAS bound to intact BRAF in an autoinhibited state with MEK1 and a 14-3-3 dimer. Analysis of this KRAS/BRAF/MEK1/14-3-3 complex reveals KRAS bound to the RAS-binding domain of BRAF, captured in two orientations. Core autoinhibitory interactions in the complex are unperturbed by binding of KRAS and in vitro activation studies confirm that KRAS binding is insufficient to activate BRAF, absent membrane recruitment. These structures illustrate the separability of binding and activation of BRAF by RAS and suggest stabilization of this pre-activation intermediate as an alternative therapeutic strategy to blocking binding of KRAS. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dgs.cif.gz | 269.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dgs.ent.gz | 211.4 KB | Display | PDB format |
PDBx/mmJSON format | 8dgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/8dgs ftp://data.pdbj.org/pub/pdb/validation_reports/dg/8dgs | HTTPS FTP |
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-Related structure data
Related structure data | 27428MC 8dgtC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 89402.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ATPgS / 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 | ||
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#2: Protein | Mass: 45835.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GDC-0623, ATPgS / 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 genetically manipulated source Source: (gene. exp.) Spodoptera exigua (beet armyworm) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V9P4T4 #4: Protein | | Mass: 21868.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GMPPNP / Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P5IP77 |
-Non-polymers , 5 types, 8 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-LCJ / | #9: Chemical | ChemComp-GNP / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Kinase Complex state-1 / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: 0.225 MDa / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER | ||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 45.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69377 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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