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Yorodumi- PDB-3e0g: Structure of the Leukemia Inhibitory Factor Receptor (LIF-R) doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e0g | |||||||||
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Title | Structure of the Leukemia Inhibitory Factor Receptor (LIF-R) domains D1-D5 | |||||||||
Components | Leukemia inhibitory factor receptor | |||||||||
Keywords | SIGNALING PROTEIN/CYTOKINE / Ig domain / Cytokine Binding Homology Region (CHR) / Cell membrane / Disease mutation / Glycoprotein / Membrane / Receptor / Secreted / Transmembrane / SIGNALING PROTEIN-CYTOKINE COMPLEX | |||||||||
Function / homology | Function and homology information leukemia inhibitory factor receptor activity / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor binding / leukemia inhibitory factor signaling pathway / RUNX1 regulates transcription of genes involved in interleukin signaling / ciliary neurotrophic factor-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / cytokine binding / growth factor binding ...leukemia inhibitory factor receptor activity / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor binding / leukemia inhibitory factor signaling pathway / RUNX1 regulates transcription of genes involved in interleukin signaling / ciliary neurotrophic factor-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / cytokine binding / growth factor binding / response to cytokine / cytokine-mediated signaling pathway / cell surface receptor signaling pathway / receptor complex / external side of plasma membrane / positive regulation of cell population proliferation / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Lupardus, P.J. / Garcia, K.C. | |||||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Structural organization of a full-length gp130/LIF-R cytokine receptor transmembrane complex. Authors: Skiniotis, G. / Lupardus, P.J. / Martick, M. / Walz, T. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e0g.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e0g.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0g ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54914.973 Da / Num. of mol.: 1 / Fragment: UNP residues 52 to 534 / Mutation: N19Q/N40Q/N95Q/N143Q/N195Q Source method: isolated from a genetically manipulated source Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus Source: (gene. exp.) Homo sapiens (human) / Gene: LIFR / Plasmid: pACGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HiFive / References: UniProt: P42702 | ||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M Sodium Citrate pH 5.0, 0.1 M Lithium Sulfate, 8% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 16991 / % possible obs: 98.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 74.762 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2 / Num. unique all: 2480 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: mouse LIF-R Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.868 / SU B: 60.725 / SU ML: 0.476 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.338 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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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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