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Yorodumi- PDB-3ncc: A human Prolactin receptor antagonist in complex with the mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ncc | ||||||
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Title | A human Prolactin receptor antagonist in complex with the mutant extracellular domain H188A of the human prolactin receptor | ||||||
Components |
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Keywords | HORMONE/HORMONE RECEPTOR / pH dependence / hematopoietic cytokine / HORMONE-HORMONE RECEPTOR complex | ||||||
Function / homology | Function and homology information prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / steroid biosynthetic process / activation of Janus kinase activity ...prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / steroid biosynthetic process / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of endothelial cell proliferation / cytokine binding / Prolactin receptor signaling / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / mammary gland alveolus development / regulation of cell adhesion / positive regulation of B cell proliferation / Growth hormone receptor signaling / embryo implantation / positive regulation of protein autophosphorylation / lactation / negative regulation of angiogenesis / response to nutrient levels / female pregnancy / endosome lumen / response to bacterium / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / receptor complex / Amyloid fiber formation / external side of plasma membrane / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / cell surface / extracellular space / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Kulkarni, M.V. / Tettamanzi, M.C. / Murphy, J.W. / Keeler, C. / Myszka, D.G. / Chayen, N.E. / Lolis, E.J. / Hodsdon, M.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation. Authors: Kulkarni, M.V. / Tettamanzi, M.C. / Murphy, J.W. / Keeler, C. / Myszka, D.G. / Chayen, N.E. / Lolis, E.J. / Hodsdon, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ncc.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ncc.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ncc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/3ncc ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3ncc | HTTPS FTP |
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-Related structure data
Related structure data | 3mzgSC 3n06C 3n0pC 3ncbC 3nceC 3ncfC 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21791.883 Da / Num. of mol.: 1 / Fragment: sequence database residues 43-227 / Mutation: G129R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hPRL, PRL / Plasmid: pT7L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01236 |
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#2: Protein | Mass: 24378.771 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 26-234 / Mutation: H188A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hPRLr, PRLR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16471 |
-Non-polymers , 4 types, 234 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-CO3 / | #6: 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: 3.48 Å3/Da / Density % sol: 64.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.7M NaCl, 0.1 M Hepes 7.5, 6% PEG monomethylether 550, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2010 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→33 Å / Num. obs: 30305 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 8 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 31.52 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MZG Resolution: 2.5→32.03 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 7.314 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.249 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.988 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→32.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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