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Yorodumi- PDB-7aam: Crystal structure of the F-BAR domain of PSTIPIP1 bound to the CT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aam | ||||||
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Title | Crystal structure of the F-BAR domain of PSTIPIP1 bound to the CTH domain of the phosphatase LYP | ||||||
Components |
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Keywords | SIGNALING PROTEIN / pyogenic arthritis / pyoderma gangrenosum and acne (PAPA) / Inflammatory response / membrane binding | ||||||
Function / homology | Function and homology information phosphoanandamide dephosphorylation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / uropod / negative regulation of T cell activation ...phosphoanandamide dephosphorylation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / uropod / negative regulation of T cell activation / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of interleukin-8 production / negative regulation of JUN kinase activity / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of T cell receptor signaling pathway / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / negative regulation of interleukin-6 production / cleavage furrow / The NLRP3 inflammasome / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / T cell differentiation / positive regulation of type I interferon production / Purinergic signaling in leishmaniasis infection / lipopolysaccharide-mediated signaling pathway / actin filament polymerization / protein dephosphorylation / negative regulation of autophagy / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / actin filament / lipid metabolic process / cytoplasmic side of plasma membrane / kinase binding / autophagy / SH3 domain binding / endocytosis / positive regulation of type II interferon production / actin filament binding / lamellipodium / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / negative regulation of gene expression / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Manso, J.A. / Alcon, P. / Bayon, Y. / Alonso, A. / de Pereda, J.M. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Cell.Mol.Life Sci. / Year: 2022 Title: PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders. Authors: Manso, J.A. / Marcos, T. / Ruiz-Martin, V. / Casas, J. / Alcon, P. / Sanchez Crespo, M. / Bayon, Y. / de Pereda, J.M. / Alonso, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aam.cif.gz | 293 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aam.ent.gz | 196.4 KB | Display | PDB format |
PDBx/mmJSON format | 7aam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/7aam ftp://data.pdbj.org/pub/pdb/validation_reports/aa/7aam | HTTPS FTP |
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-Related structure data
Related structure data | 7aalC 7aanSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3876245 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 34260.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSTPIP1, CD2BP1 / Plasmid: pETEV15b / Details (production host): Based on pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43586 #2: Protein/peptide | | Mass: 2385.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.5 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Bis-Tris-propane (pH=6.0), 20% (w/v) PEG 3350, 200 mM sodium citrate. LYP-CTH peptide was soaked into preformed crystals of the F-BAR domain of PSTPIP1. |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→102.52 Å / Num. obs: 20328 / % possible obs: 51.5 % / Redundancy: 19.1 % / Biso Wilson estimate: 24.23 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.397 / Rrim(I) all: 0.407 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.154→2.316 Å / Redundancy: 17.8 % / Rmerge(I) obs: 3.036 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1016 / CC1/2: 0.521 / Rpim(I) all: 0.722 / % possible all: 13.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7AAN Resolution: 2.15→102.52 Å / SU ML: 0.2541 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8806 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→102.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.22149842685 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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