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Yorodumi- PDB-1kf9: PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kf9 | ||||||
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Title | PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / CYTOKINE / HORMONE-RECEPTOR COMPLEX / PHAGE DISPLAY MOLECULAR PLASTICITY / RECEPTOR HOMODIMERIZATION / HUMAN GROWTH HORMONE / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information growth hormone receptor activity / regulation of response to nutrient levels / growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / positive regulation of growth / taurine metabolic process / animal organ development / positive regulation of activation of Janus kinase activity ...growth hormone receptor activity / regulation of response to nutrient levels / growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / positive regulation of growth / taurine metabolic process / animal organ development / positive regulation of activation of Janus kinase activity / response to gravity / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / hormone metabolic process / positive regulation of glucose transmembrane transport / proline-rich region binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor binding / response to food / growth hormone receptor signaling pathway / response to cycloheximide / Prolactin receptor signaling / cytokine binding / growth factor binding / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / regulation of multicellular organism growth / Synthesis, secretion, and deacylation of Ghrelin / Growth hormone receptor signaling / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to hormone stimulus / hormone-mediated signaling pathway / response to interleukin-1 / SH2 domain binding / response to nutrient levels / insulin-like growth factor receptor signaling pathway / cytokine activity / endosome lumen / positive regulation of cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of MAP kinase activity / growth factor activity / hormone activity / receptor internalization / cytokine-mediated signaling pathway / cytoplasmic ribonucleoprotein granule / endocytosis / cellular response to insulin stimulus / positive regulation of peptidyl-tyrosine phosphorylation / response to estradiol / protein phosphatase binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / external side of plasma membrane / neuronal cell body / lipid binding / protein kinase binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Schiffer, C.A. / Ultsch, M. / Walsh, S. / Somers, W. / De Vos, A.M. / Kossiakoff, A.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structure of a Phage Display Derived Variant of Human Growth Hormone Complexed to Two Copies of the Extracellular Domain of its Receptor: Evidence for Strong Structural Coupling between Receptor Binding Sites Authors: Schiffer, C.A. / Ultsch, M. / Walsh, S. / Somers, W. / De Vos, A.M. / Kossiakoff, A.A. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the molecules A and D have not been deposited in any sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kf9.cif.gz | 223.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kf9.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kf9_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 1kf9_full_validation.pdf.gz | 476.2 KB | Display | |
Data in XML | 1kf9_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 1kf9_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/1kf9 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/1kf9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21986.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01241*PLUS #2: Protein | Mass: 27409.771 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10912 #3: 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: 2.34 Å3/Da / Density % sol: 47.32 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.3 / Details: pH 6.30 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.3 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 43162 / % possible obs: 95.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 215604 |
Reflection shell | *PLUS % possible obs: 78.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 47.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |