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Yorodumi- PDB-1c1y: CRYSTAL STRUCTURE OF RAP.GMPPNP IN COMPLEX WITH THE RAS-BINDING-D... -
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-Basic information
Entry | Database: PDB / ID: 1c1y | ||||||
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Title | CRYSTAL STRUCTURE OF RAP.GMPPNP IN COMPLEX WITH THE RAS-BINDING-DOMAIN OF C-RAF1 KINASE (RAFRBD). | ||||||
Components |
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Keywords | SIGNALING PROTEIN / GTP-BINDING PROTEINS / PROTEIN-PROTEIN COMPLEX / EFFECTORS | ||||||
Function / homology | Function and homology information Rap protein signal transduction / death-inducing signaling complex assembly / regulation of cell junction assembly / nerve growth factor signaling pathway / intermediate filament cytoskeleton organization / positive regulation of vasculogenesis / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation / regulation of Rho protein signal transduction ...Rap protein signal transduction / death-inducing signaling complex assembly / regulation of cell junction assembly / nerve growth factor signaling pathway / intermediate filament cytoskeleton organization / positive regulation of vasculogenesis / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / anchoring junction / establishment of endothelial barrier / insulin secretion involved in cellular response to glucose stimulus / MET activates RAP1 and RAC1 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Negative feedback regulation of MAPK pathway / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / Frs2-mediated activation / p130Cas linkage to MAPK signaling for integrins / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / face development / synaptic vesicle exocytosis / pseudopodium / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / thyroid gland development / GRB2:SOS provides linkage to MAPK signaling for Integrins / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / positive regulation of protein kinase activity / negative regulation of protein-containing complex assembly / specific granule membrane / Schwann cell development / type II interferon-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cAMP / sperm midpiece / response to muscle stretch / activation of adenylate cyclase activity / myelination / CD209 (DC-SIGN) signaling / Integrin signaling / guanyl-nucleotide exchange factor activity / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / thymus development / protein localization to plasma membrane / 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 / positive regulation of neuron projection development / Stimuli-sensing channels / small GTPase binding / positive regulation of GTPase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Negative regulation of MAPK pathway / GDP binding / 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 / late endosome / presynapse / insulin receptor signaling pathway / cell junction / positive regulation of peptidyl-serine phosphorylation / nervous system development / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / GTPase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / protein-containing complex binding / GTP binding / negative regulation of apoptotic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Nassar, N. | ||||||
Citation | Journal: Nature / Year: 1995 Title: The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Authors: Nassar, N. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Ras/Rap effector specificty determined by charge reversal. Authors: Nassar, N. #2: Journal: Nature / Year: 2008 Title: Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B. Authors: Holger Rehmann / Ernesto Arias-Palomo / Michael A Hadders / Frank Schwede / Oscar Llorca / Johannes L Bos / Abstract: Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell ...Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c1y.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c1y.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 1c1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c1y ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c1y | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 19055.641 Da / Num. of mol.: 1 / Fragment: RAP, RESIDUES 1-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBKS / Production host: Escherichia coli (E. coli) / References: UniProt: P62834 |
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#2: Protein | Mass: 8789.290 Da / Num. of mol.: 1 / Fragment: RAFRBD, RESIDUES 51-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) References: UniProt: P04049, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
-Non-polymers , 4 types, 86 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GTP / |
#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: mmePeg5000, magnesium chloride, calcium chloride, ammonium sulphate., pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 24787 / Num. obs: 24787 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.325 / Num. unique all: 3569 / % possible all: 93.6 |
Reflection | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 7734287.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum Likelyhood refinement using CNS_0.4.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.03 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.38 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.357 |