+Open data
-Basic information
Entry | Database: PDB / ID: 2b9j | ||||||
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Title | Crystal structure of Fus3 with a docking motif from Far1 | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information MAPK3 (ERK1) activation / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Frs2-mediated activation / ERK/MAPK targets / Signalling to ERK5 / ERKs are inactivated / Senescence-Associated Secretory Phenotype (SASP) / NCAM signaling for neurite out-growth ...MAPK3 (ERK1) activation / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Frs2-mediated activation / ERK/MAPK targets / Signalling to ERK5 / ERKs are inactivated / Senescence-Associated Secretory Phenotype (SASP) / NCAM signaling for neurite out-growth / Recycling pathway of L1 / Signal transduction by L1 / RAF/MAP kinase cascade / MAP2K and MAPK activation / Negative feedback regulation of MAPK pathway / Negative regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-stimulated signaling through PRKCZ / Ca2+ pathway / pheromone response MAPK cascade / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / Regulation of HSF1-mediated heat shock response / Activation of the AP-1 family of transcription factors / retrotransposon silencing / mating projection tip / negative regulation of MAPK cascade / MAPK6/MAPK4 signaling / MAP kinase activity / mitogen-activated protein kinase / Neutrophil degranulation / positive regulation of protein export from nucleus / cytoplasmic stress granule / periplasmic space / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Remenyi, A. / Good, M.C. / Bhattacharyya, R.P. / Lim, W.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network. Authors: Remenyi, A. / Good, M.C. / Bhattacharyya, R.P. / Lim, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b9j.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b9j.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b9j_validation.pdf.gz | 738.5 KB | Display | wwPDB validaton report |
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Full document | 2b9j_full_validation.pdf.gz | 744.9 KB | Display | |
Data in XML | 2b9j_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 2b9j_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/2b9j ftp://data.pdbj.org/pub/pdb/validation_reports/b9/2b9j | HTTPS FTP |
-Related structure data
Related structure data | 2b9fSC 2b9hC 2b9iC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 40809.047 Da / Num. of mol.: 1 / Mutation: T180V, Y182F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FUS3, DAC2 / Plasmid: pBH4-Fus3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)plysS / References: UniProt: P16892, EC: 2.7.1.37 |
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#2: Protein/peptide | Mass: 1426.685 Da / Num. of mol.: 1 / Fragment: Far1 docking motif / Source method: obtained synthetically Details: The Far1 docking motif was chemically synthesized. The sequence of this peptide naturally exists in Saccharomyces cerevisiae (Baker's yeast). |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 15-20% PEG8000, 0.1M MES pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 16794 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rsym value: 0.09 / Net I/σ(I): 12.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2B9F Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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