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Yorodumi- PDB-3maz: Crystal Structure of the Human BRDG1/STAP-1 SH2 Domain in Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3maz | ||||||
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Title | Crystal Structure of the Human BRDG1/STAP-1 SH2 Domain in Complex with the NTAL pTyr136 Peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / modular domain / phosphotyrosine / specificity / Cytoplasm / Phosphoprotein / SH2 domain | ||||||
Function / homology | Function and homology information negative regulation of microglial cell migration / mast cell granule / negative regulation of macrophage colony-stimulating factor signaling pathway / macrophage colony-stimulating factor receptor binding / negative regulation of ruffle assembly / positive regulation of B cell receptor signaling pathway / positive regulation of microglial cell mediated cytotoxicity / positive regulation of microglial cell activation / positive regulation of phagocytosis, engulfment / negative regulation of phosphorylation ...negative regulation of microglial cell migration / mast cell granule / negative regulation of macrophage colony-stimulating factor signaling pathway / macrophage colony-stimulating factor receptor binding / negative regulation of ruffle assembly / positive regulation of B cell receptor signaling pathway / positive regulation of microglial cell mediated cytotoxicity / positive regulation of microglial cell activation / positive regulation of phagocytosis, engulfment / negative regulation of phosphorylation / negative regulation of macrophage chemotaxis / transmembrane receptor protein tyrosine kinase adaptor activity / mast cell degranulation / B cell activation / protein tyrosine kinase activator activity / Fc-epsilon receptor signaling pathway / centriolar satellite / Role of LAT2/NTAL/LAB on calcium mobilization / signaling adaptor activity / phosphotyrosine residue binding / SH2 domain binding / calcium-mediated signaling / B cell receptor signaling pathway / phospholipid binding / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to lipopolysaccharide / adaptive immune response / membrane => GO:0016020 / intracellular signal transduction / membrane raft / positive regulation of gene expression / protein kinase binding / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kaneko, T. / Huang, H. / Zhao, B. / Li, L. / Liu, H. / Voss, C.K. / Wu, C. / Schiller, M.R. / Li, S.S. | ||||||
Citation | Journal: Sci.Signal. / Year: 2010 Title: Loops govern SH2 domain specificity by controlling access to binding pockets. Authors: Kaneko, T. / Huang, H. / Zhao, B. / Li, L. / Liu, H. / Voss, C.K. / Wu, C. / Schiller, M.R. / Li, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3maz.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3maz.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 3maz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3maz ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3maz | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14180.105 Da / Num. of mol.: 1 / Fragment: UNP Residues 167-285, SH2 domain / Mutation: C269A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAP1, BRDG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULZ2 |
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#2: Protein/peptide | Mass: 1300.355 Da / Num. of mol.: 1 / Mutation: C142A / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q9GZY6 |
#3: Chemical | ChemComp-MLI / |
#4: 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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 2.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2008 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24.3 Å / Num. all: 12591 / Num. obs: 12585 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.4 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1BMB 1H9O 1I3Z 1KC2 Resolution: 1.9→24.27 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1413652.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.2015 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.27 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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