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Yorodumi- PDB-6xha: Crystal Structure of KRAS-G12V (GMPPNP-bound) in complex with RAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xha | ||||||
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Title | Crystal Structure of KRAS-G12V (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF | ||||||
Components |
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Keywords | ONCOPROTEIN/Transferase / KRAS / RAS / K-ras / KRAS4b / G12V / RAF1 / CRAF / RBD / RAS-binding domain / cysteine-rich domain / CRD / ONCOPROTEIN / ONCOPROTEIN-Transferase complex | ||||||
Function / homology | Function and homology information death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / face development / pseudopodium / somatic stem cell population maintenance / thyroid gland development / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / negative regulation of protein-containing complex assembly / Schwann cell development / type II interferon-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / activation of adenylate cyclase activity / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / small monomeric GTPase / insulin-like growth factor receptor signaling pathway / thymus development / RAF activation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Stimuli-sensing channels / 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 / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / Ca2+ pathway / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | Tran, T.H. / Chan, A.H. / Dharmaiah, S. / Simanshu, D.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Authors: Tran, T.H. / Chan, A.H. / Young, L.C. / Bindu, L. / Neale, C. / Messing, S. / Dharmaiah, S. / Taylor, T. / Denson, J.P. / Esposito, D. / Nissley, D.V. / Stephen, A.G. / McCormick, F. / Simanshu, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xha.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xha.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xha ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xha | HTTPS FTP |
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-Related 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: 19354.824 Da / Num. of mol.: 1 / Mutation: G12V, C118S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116-2, small monomeric GTPase |
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#2: Protein | Mass: 15888.440 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Escherichia coli (E. coli) References: UniProt: P04049, non-specific serine/threonine protein kinase |
-Non-polymers , 6 types, 22 molecules
#3: Chemical | ChemComp-GNP / | ||||||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-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: 3.23 Å3/Da / Density % sol: 61.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM sodium cacodylate pH 6.5, 200 mM MgCl2, 8% PGA, 0.35 mM D-myo-phosphatidylinositol 3,4,5-triphosphate |
-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: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→48.3 Å / Num. obs: 10931 / % possible obs: 98.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 82.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.079 / Net I/σ(I): 16.04 |
Reflection shell | Resolution: 2.87→2.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 1720 / CC1/2: 0.827 / Rrim(I) all: 0.965 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: KRAS:RAF1-RBDCRD (crystal form II) Resolution: 2.87→48.3 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.93 / 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: 218.6 Å2 / Biso mean: 102.9443 Å2 / Biso min: 42.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.87→48.3 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 36.7466 Å / Origin y: 40.8035 Å / Origin z: 20.4181 Å
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Refinement TLS group |
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