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Yorodumi- PDB-3n06: A mutant human Prolactin receptor antagonist H27A in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n06 | ||||||
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Title | A mutant human Prolactin receptor antagonist H27A in complex with the extracellular domain 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 / Prolactin receptor signaling / negative regulation of endothelial cell proliferation / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / peptide hormone binding / mammary gland alveolus development / regulation of cell adhesion / negative regulation of angiogenesis / Growth hormone receptor signaling / positive regulation of B cell proliferation / positive regulation of protein autophosphorylation / lactation / embryo implantation / response to nutrient levels / positive regulation of miRNA transcription / endosome lumen / female pregnancy / response to bacterium / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / positive regulation of canonical NF-kappaB signal transduction / receptor complex / cell surface receptor signaling pathway / Amyloid fiber formation / external side of plasma membrane / positive regulation of cell population proliferation / lipid binding / 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 / Resolution: 2 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 | 3n06.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n06.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n06_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 3n06_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 3n06_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 3n06_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/3n06 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/3n06 | HTTPS FTP |
-Related structure data
Related structure data | 3mzgSC 3n0pC 3ncbC 3nccC 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
#1: Protein | Mass: 21724.812 Da / Num. of mol.: 1 / Fragment: sequence database residues 43-227 / Mutation: H27A, 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: 24445.840 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 26-234 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 | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.6M NaCl, 0.1 M Hepes 7.5, 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: 1.0809 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2009 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→31 Å / Num. obs: 42787 / % possible obs: 100 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 8.5 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MZG Resolution: 2→30.857 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.144 / 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: 42.116 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30.857 Å
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LS refinement shell | Resolution: 1.998→2.05 Å / Total num. of bins used: 20
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