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Yorodumi- PDB-6qio: Ternary complex of FcRn ectodomain, FcRn binding optimised human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qio | |||||||||
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Title | Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the human growth hormone derivative somapacitan | |||||||||
Components |
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Keywords | HORMONE / complex / albumin binding / long-acting growth hormone / somapacitan | |||||||||
Function / homology | Function and homology information growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / positive regulation of growth / animal organ development / cell surface receptor signaling pathway via STAT / exogenous protein binding / positive regulation of multicellular organism growth ...growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / positive regulation of growth / animal organ development / cell surface receptor signaling pathway via STAT / exogenous protein binding / positive regulation of multicellular organism growth / Ciprofloxacin ADME / cellular response to calcium ion starvation / positive regulation of D-glucose transmembrane transport / enterobactin binding / Heme biosynthesis / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor binding / HDL remodeling / IgG binding / negative regulation of mitochondrial depolarization / Prednisone ADME / growth hormone receptor signaling pathway / Heme degradation / Aspirin ADME / Prolactin receptor signaling / antioxidant activity / cell surface receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / toxic substance binding / beta-2-microglobulin binding / growth hormone receptor signaling pathway via JAK-STAT / Scavenging of heme from plasma / positive regulation of tyrosine phosphorylation of STAT protein / Growth hormone receptor signaling / Recycling of bile acids and salts / cellular response to starvation / response to nutrient levels / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / platelet alpha granule lumen / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / cytokine activity / endosome lumen / fatty acid binding / cellular response to iron ion / Endosomal/Vacuolar pathway / positive regulation of receptor signaling pathway via JAK-STAT / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Post-translational protein phosphorylation / growth factor activity / cellular response to iron(III) ion / positive regulation of MAP kinase activity / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / hormone activity / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / cytokine-mediated signaling pathway / sensory perception of smell / MHC class I protein complex / negative regulation of neurogenesis / multicellular organismal-level iron ion homeostasis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / peptide antigen binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Modulation by Mtb of host immune system / Platelet degranulation / negative regulation of neuron projection development / pyridoxal phosphate binding / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / response to estradiol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Johansson, E. | |||||||||
Citation | Journal: Biochemistry / Year: 2020 Title: Identification of Binding Sites on Human Serum Albumin for Somapacitan, a Long-Acting Growth Hormone Derivative. Authors: Johansson, E. / Nielsen, A.D. / Demuth, H. / Wiberg, C. / Schjodt, C.B. / Huang, T. / Chen, J. / Jensen, S. / Petersen, J. / Thygesen, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qio.cif.gz | 394.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qio.ent.gz | 319.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qio_validation.pdf.gz | 523.3 KB | Display | wwPDB validaton report |
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Full document | 6qio_full_validation.pdf.gz | 539.4 KB | Display | |
Data in XML | 6qio_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 6qio_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/6qio ftp://data.pdbj.org/pub/pdb/validation_reports/qi/6qio | HTTPS FTP |
-Related structure data
Related structure data | 6qipC 4k71S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 66473.148 Da / Num. of mol.: 1 / Mutation: V418M, T420A, E505G, V547A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 Production host: Komagataella pastoris (fungus) / References: UniProt: P02768 |
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#2: Protein | Mass: 30408.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E / References: UniProt: P55899 |
#3: Protein | Mass: 12577.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E / References: UniProt: P61769 |
-Non-polymers , 4 types, 882 molecules
#4: Chemical | ChemComp-MES / | ||||
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#5: Chemical | #6: Chemical | ChemComp-JG5 / | #7: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y |
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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: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: ammonium acetate, sodium acetate, PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.85 Å / Num. obs: 95478 / % possible obs: 99.91 % / Redundancy: 6.7 % / Net I/σ(I): 11.23 |
Reflection shell | Resolution: 1.95→2.02 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K71 Resolution: 1.95→48.846 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 23.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.846 Å
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Refine LS restraints |
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LS refinement shell |
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