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Yorodumi- PDB-3ew3: the 1:2 complex between a Nterminal elongated prolactin and the e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ew3 | ||||||
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Title | the 1:2 complex between a Nterminal elongated prolactin and the extra cellular domain of the rat prolactin receptor | ||||||
Components |
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Keywords | HORMONE/HORMONE RECEPTOR / complex / Glycoprotein / Hormone / Lactation / Secreted / Alternative splicing / Membrane / Receptor / Transmembrane / HORMONE-HORMONE RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / Growth hormone receptor signaling / regulation of epithelial cell differentiation / prolactin signaling pathway / mammary gland epithelium development / prostate gland growth / mammary gland epithelial cell differentiation ...Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / Growth hormone receptor signaling / regulation of epithelial cell differentiation / prolactin signaling pathway / mammary gland epithelium development / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / 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 / 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) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å | ||||||
Authors | Broutin, I. / Jomain, J.B. / England, P. / Goffin, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2. Authors: Broutin, I. / Jomain, J.B. / Tallet, E. / van Agthoven, J. / Raynal, B. / Hoos, S. / Kragelund, B.B. / Kelly, P.A. / Ducruix, A. / England, P. / Goffin, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ew3.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ew3.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 3ew3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ew3_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 3ew3_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 3ew3_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3ew3_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/3ew3 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/3ew3 | HTTPS FTP |
-Related structure data
Related structure data | 1f6fS S: Starting model for refinement |
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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: 23613.959 Da / Num. of mol.: 1 / Fragment: UNP residues 43-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRL / Plasmid: PQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01236 | ||
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#2: Protein | Mass: 26033.115 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prlr / Plasmid: pRc/CMV / Production host: Escherichia coli (E. coli) / Strain (production host): M15-rep4 / References: UniProt: P05710 Sequence details | FIRST 14 AA REPLACED BY N-TERMINUS 17 AA FROM OPL: P16038 CSH_SHEEP | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.34 % / Mosaicity: 1.053 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100mM LiSO4, 100mM NaCitrate pH 5.6, 12% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2006 / Details: mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: torodial focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→107.833 Å / Num. obs: 10464 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.536 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 1F6F Resolution: 3.8→14.997 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.684 / SU ML: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.41 / σ(I): 0 / Phase error: 35.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 41.849 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.74 Å2 / Biso mean: 43.14 Å2 / Biso min: 12.99 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→14.997 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Xplor file | Serial no: 1 / Param file: protein_rep.param |