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Yorodumi- PDB-1gua: HUMAN RAP1A, RESIDUES 1-167, DOUBLE MUTANT (E30D,K31E) COMPLEXED ... -
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-Basic information
Entry | Database: PDB / ID: 1gua | ||||||
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Title | HUMAN RAP1A, RESIDUES 1-167, DOUBLE MUTANT (E30D,K31E) COMPLEXED WITH GPPNHP AND THE RAS-BINDING-DOMAIN OF HUMAN C-RAF1, RESIDUES 51-131 | ||||||
Components |
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Keywords | COMPLEX (GTP-BINDING/ATP-BINDING) / ONCOGENE PROTEIN/KINASE/EFFECTOR PROTEIN GTP-BINDING-PROTEIN / COMPLEX (GTP-BINDING-ATP-BINDING) / COMPLEX (GTP-BINDING-ATP-BINDING) complex | ||||||
Function / homology | Function and homology information Rap protein signal transduction / death-inducing signaling complex assembly / regulation of cell junction assembly / intermediate filament cytoskeleton organization / nerve growth factor signaling pathway / positive regulation of vasculogenesis / negative regulation of synaptic vesicle exocytosis / guanyl-nucleotide exchange factor complex / 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 / intermediate filament cytoskeleton organization / nerve growth factor signaling pathway / positive regulation of vasculogenesis / negative regulation of synaptic vesicle exocytosis / guanyl-nucleotide exchange factor complex / 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 / establishment of endothelial barrier / insulin secretion involved in cellular response to glucose stimulus / anchoring junction / MET activates RAP1 and RAC1 / MAP kinase kinase kinase activity / 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 / pseudopodium / synaptic vesicle exocytosis / somatic stem cell population maintenance / thyroid gland development / GRB2:SOS provides linkage to MAPK signaling for Integrins / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein kinase activity / negative regulation of protein-containing complex assembly / Schwann cell development / specific granule membrane / type II interferon-mediated signaling pathway / activation of adenylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cAMP / sperm midpiece / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / Integrin signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / insulin-like growth factor receptor signaling pathway / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / positive regulation of GTPase activity / thymus development / guanyl-nucleotide exchange factor activity / protein localization to plasma membrane / RAF activation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Stimuli-sensing channels / small GTPase binding / positive regulation of neuron projection development / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / 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 / GDP binding / cell junction / positive regulation of peptidyl-serine phosphorylation / MAPK cascade / Signaling by BRAF and RAF1 fusions / late endosome / insulin receptor signaling pathway / presynapse / nervous system development / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / endosome membrane / early endosome / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / protein phosphorylation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / glutamatergic synapse / Neutrophil degranulation / negative regulation of apoptotic process / protein-containing complex binding / GTP binding / apoptotic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Nassar, N. / Wittinghofer, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Ras/Rap effector specificity determined by charge reversal. Authors: Nassar, N. / Horn, G. / Herrmann, C. / Block, C. / Janknecht, R. / Wittinghofer, A. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Quantitative Structure-Activity Analysis Correlating Ras/Raf Interaction in Vitro to Raf Activation in Vivo Authors: Block, C. / Janknecht, R. / Herrmann, C. / Nassar, N. / Wittinghofer, A. #2: Journal: J.Biol.Chem. / Year: 1995 Title: Quantitative Analysis of the Complex between P21Ras and the Ras-Binding Domain of the Human Raf-1 Protein Kinase Authors: Herrmann, C. / Martin, G.A. / Wittinghofer, A. #3: 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. / Horn, G. / Herrmann, C. / Scherer, A. / Mccormick, F. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gua.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gua.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gua_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
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Full document | 1gua_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 1gua_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1gua_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1gua ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gua | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 19041.549 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-167 / Mutation: E30D, K31E, DEL(168-186) Source method: isolated from a genetically manipulated source Details: COMPLEXED TO 5'-GUANOSYL-IMIDO-TRIPHOSPHATE / Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN C-RAF1 GENE RESIDUES 51 / Plasmid: PTAC / Gene (production host): HUMAN RAP1A GENE / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P62834 |
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#2: Protein | Mass: 9203.765 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-131 Source method: isolated from a genetically manipulated source Details: HUMAN RAP1A AND C-RAF1 / Source: (gene. exp.) Homo sapiens (human) Description: PURIFIED AS A GST-FUSION PROTEIN WITH THROMBIN CLEAVAGE SITE Gene: HUMAN C-RAF1 GENE RESIDUES 51 / Plasmid: PGEX-RAFRBD / Species (production host): Escherichia coli / Gene (production host): HUMAN C-RAF1 GENE, RESIDUES 51-131 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P04049, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
-Non-polymers , 4 types, 92 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GNP / |
#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 21975 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.049 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 26720 / Rmerge(I) obs: 0.041 |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 0 Details: THE ELECTRON DENSITY FOR THE SIDE CHAINS OF RESIDUES 104 - 107 FROM RBD (CHAIN B) IS WEAK.
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Displacement parameters | Biso mean: 16.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |