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Yorodumi- PDB-4wo1: Crystal structure of the DAP12 transmembrane domain in lipid cubi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wo1 | ||||||||||||
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Title | Crystal structure of the DAP12 transmembrane domain in lipid cubic phase | ||||||||||||
Components | TYRO protein tyrosine kinase-binding protein | ||||||||||||
Keywords | SIGNALING PROTEIN / alpha-helix Transmembrane Signaling | ||||||||||||
Function / homology | Function and homology information myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / Other semaphorin interactions / positive regulation of microglial cell mediated cytotoxicity ...myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / Other semaphorin interactions / positive regulation of microglial cell mediated cytotoxicity / neutrophil activation involved in immune response / positive regulation of protein localization to cell surface / apoptotic cell clearance / Signal regulatory protein family interactions / negative regulation of type I interferon production / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / stimulatory C-type lectin receptor signaling pathway / negative regulation of long-term synaptic potentiation / response to axon injury / cellular defense response / forebrain development / osteoclast differentiation / positive regulation of superoxide anion generation / secretory granule membrane / positive regulation of interleukin-1 beta production / DAP12 interactions / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / actin cytoskeleton organization / molecular adaptor activity / protein stabilization / intracellular signal transduction / signaling receptor binding / Neutrophil degranulation / positive regulation of gene expression / cell surface / signal transduction / protein homodimerization activity / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||||||||
Authors | Call, M.J. / Call, M.E. / Knoblich, K. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Cell Rep / Year: 2015 Title: Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly. Authors: Knoblich, K. / Park, S. / Lutfi, M. / van 't Hag, L. / Conn, C.E. / Seabrook, S.A. / Newman, J. / Czabotar, P.E. / Im, W. / Call, M.E. / Call, M.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wo1.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wo1.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wo1_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4wo1_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4wo1_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4wo1_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/4wo1 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4wo1 | HTTPS FTP |
-Related structure data
Related structure data | 4wolSC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3331.042 Da / Num. of mol.: 4 / Fragment: UNP residues 35-67 / Mutation: M21V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYROBP, DAP12, KARAP / Production host: Escherichia coli (E. coli) / References: UniProt: O43914 #2: Chemical | ChemComp-CA / | #3: Chemical | ChemComp-OLC / ( #4: Water | ChemComp-HOH / | |
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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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.07 Details: 0.1 M bis-tris propane chloride pH 6.07, 19.7 %w/v PEG 3350, 0.27 M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→33.12 Å / Num. obs: 6316 / % possible obs: 95.74 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1374 / Net I/σ(I): 15.46 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WOL Resolution: 2.14→33.121 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.79 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→33.121 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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