[English] 日本語
![](img/lk-miru.gif)
- PDB-3ncc: A human Prolactin receptor antagonist in complex with the mutant ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ncc | ||||||
---|---|---|---|---|---|---|---|
Title | A human Prolactin receptor antagonist in complex with the mutant extracellular domain H188A of the human prolactin receptor | ||||||
![]() |
| ||||||
![]() | HORMONE/HORMONE RECEPTOR / pH dependence / hematopoietic cytokine / HORMONE-HORMONE RECEPTOR complex | ||||||
Function / homology | ![]() 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 / cytokine binding / Prolactin receptor signaling / negative regulation of endothelial cell proliferation / cell surface receptor signaling pathway via JAK-STAT / peptide hormone binding / mammary gland alveolus development / regulation of cell adhesion / Growth hormone receptor signaling / positive regulation of B cell proliferation / positive regulation of protein autophosphorylation / lactation / embryo implantation / negative regulation of angiogenesis / response to nutrient levels / 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 miRNA transcription / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kulkarni, M.V. / Tettamanzi, M.C. / Murphy, J.W. / Keeler, C. / Myszka, D.G. / Chayen, N.E. / Lolis, E.J. / Hodsdon, M.E. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.7 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mzgSC ![]() 3n06C ![]() 3n0pC ![]() 3ncbC ![]() 3nceC ![]() 3ncfC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 234 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-CO3 / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.68 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||
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 |
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 31.52 / Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→32.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
|