+Open data
-Basic information
Entry | Database: PDB / ID: 6e2p | ||||||
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Title | Structure of human JAK2 FERM/SH2 in complex with Leptin Receptor | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Cytokine Receptor / Leptin / Signal Transduction | ||||||
Function / homology | Function and homology information regulation of transport / leptin receptor activity / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / sexual reproduction / regulation of feeding behavior / multicellular organism development / interleukin-35-mediated signaling pathway ...regulation of transport / leptin receptor activity / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / sexual reproduction / regulation of feeding behavior / multicellular organism development / interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / energy reserve metabolic process / Signaling by Erythropoietin / collagen-activated signaling pathway / interleukin-12 receptor binding / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / response to interleukin-12 / Erythropoietin activates Phospholipase C gamma (PLCG) / positive regulation of leukocyte proliferation / post-embryonic hemopoiesis / interleukin-12 receptor complex / activation of Janus kinase activity / tyrosine phosphorylation of STAT protein / interleukin-23 receptor complex / positive regulation of MHC class II biosynthetic process / positive regulation of platelet aggregation / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of platelet activation / acetylcholine receptor binding / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / Signaling by Leptin / regulation of nitric oxide biosynthetic process / positive regulation of signaling receptor activity / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / positive regulation of epithelial cell apoptotic process / response to hydroperoxide / positive regulation of natural killer cell proliferation / positive regulation of cell-substrate adhesion / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / axon regeneration / growth hormone receptor signaling pathway / peptide hormone receptor binding / cytokine receptor activity / negative regulation of cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic component of plasma membrane / IFNG signaling activates MAPKs / glycogen metabolic process / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / negative regulation of cell-cell adhesion / Interleukin-6 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / enzyme-linked receptor protein signaling pathway / cytokine binding / Prolactin receptor signaling / MAPK3 (ERK1) activation / response to amine / positive regulation of interleukin-17 production / negative regulation of DNA binding / positive regulation of nitric-oxide synthase biosynthetic process / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / mesoderm development / positive regulation of SMAD protein signal transduction / platelet-derived growth factor receptor signaling pathway / transport across blood-brain barrier / T cell differentiation / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / glial cell proliferation / growth hormone receptor signaling pathway via JAK-STAT / response to tumor necrosis factor / Interleukin receptor SHC signaling / negative regulation of gluconeogenesis / phosphatidylinositol 3-kinase binding / phagocytosis / energy homeostasis / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / Erythropoietin activates RAS Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Ferrao, R. / Lupardus, P.J. / Wallweber, H.J.A. | ||||||
Citation | Journal: Elife / Year: 2018 Title: Receptor-mediated dimerization of JAK2 FERM domains is required for JAK2 activation. Authors: Ferrao, R.D. / Wallweber, H. / Lupardus, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e2p.cif.gz | 402.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e2p.ent.gz | 331.4 KB | Display | PDB format |
PDBx/mmJSON format | 6e2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e2p_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
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Full document | 6e2p_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 6e2p_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 6e2p_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/6e2p ftp://data.pdbj.org/pub/pdb/validation_reports/e2/6e2p | HTTPS FTP |
-Related structure data
Related structure data | 6e2qC 4z32S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 55919.613 Da / Num. of mol.: 2 / Fragment: FERM/SH2 (UNP residues 36-514) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAK2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O60674, non-specific protein-tyrosine kinase #2: Protein | Mass: 8584.573 Da / Num. of mol.: 2 / Fragment: UNP residues 863-933 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LEPR, DB, OBR / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P48357 #3: Chemical | ChemComp-SO4 / | #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: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, pH 6.5, 0.2 M magnesium chloride, 5-10% PEG4000, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→43.19 Å / Num. obs: 49544 / % possible obs: 99.58 % / Redundancy: 13.4 % / Biso Wilson estimate: 78.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1052 / Rpim(I) all: 0.02946 / Rrim(I) all: 0.1093 / Net I/σ(I): 21.83 |
Reflection shell | Resolution: 2.83→2.931 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.597 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 4861 / CC1/2: 0.798 / Rpim(I) all: 0.4413 / Rrim(I) all: 1.658 / % possible all: 99.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4Z32 Resolution: 2.83→43.186 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→43.186 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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