+Open data
-Basic information
Entry | Database: PDB / ID: 4yfd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/HYDROLASE / trans-synaptic complex / synapse organizer / IMMUNE SYSTEM-HYDROLASE complex | ||||||
Function / homology | Function and homology information Interleukin-36 pathway / Interleukin-33 signaling / interleukin-33 receptor activity / interleukin-1 receptor activity / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / NADP+ nucleosidase activity ...Interleukin-36 pathway / Interleukin-33 signaling / interleukin-33 receptor activity / interleukin-1 receptor activity / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / NADP+ nucleosidase activity / regulation of postsynaptic density assembly / synaptic membrane adhesion / Interleukin-1 signaling / PIP3 activates AKT signaling / interleukin-33-mediated signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / negative regulation of receptor signaling pathway via JAK-STAT / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / interleukin-1 receptor binding / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / interleukin-1-mediated signaling pathway / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of interleukin-4 production / regulation of presynapse assembly / regulation of immune response / coreceptor activity / dephosphorylation / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / presynaptic membrane / positive regulation of NF-kappaB transcription factor activity / receptor complex / inflammatory response / innate immune response / signaling receptor binding / glutamatergic synapse / synapse / protein-containing complex / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.253 Å | ||||||
Authors | Yamagata, A. / Fukai, S. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation. Authors: Yamagata, A. / Yoshida, T. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Iwasawa-Okamoto, S. / Mori, H. / Mishina, M. / Fukai, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yfd.cif.gz | 345.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yfd.ent.gz | 281.9 KB | Display | PDB format |
PDBx/mmJSON format | 4yfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yfd_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4yfd_full_validation.pdf.gz | 491.1 KB | Display | |
Data in XML | 4yfd_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 4yfd_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfd ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfd | HTTPS FTP |
-Related structure data
Related structure data | 4yfeSC 4yfgC 4yh6C 4yh7C 5y32C 2yd6S 2yd9S 3o4oS 4depS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39368.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il1rap / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q61730 |
---|---|
#2: Protein | Mass: 53912.441 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase |
#3: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.67 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% PEG3350, 0.1 M ammonium sulfate and 0.1 M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 25436 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rsym value: 0.118 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.25→3.31 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / % possible all: 92.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YD6, 2YD9, 4DEP, 3O4O, 4YFE Resolution: 3.253→48.974 Å / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 33.03 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.253→48.974 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.6804 Å / Origin y: 14.5936 Å / Origin z: 31.1471 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |