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Yorodumi- PDB-4k71: Crystal structure of a high affinity Human Serum Albumin variant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k71 | ||||||
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Title | Crystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc Receptor | ||||||
Components |
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Keywords | LIPID TRANSPORT / MHC Class I / Endosome Recycling / Endosome | ||||||
Function / homology | Function and homology information IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / IgG binding / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / IgG binding / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / beta-2-microglobulin binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / platelet alpha granule lumen / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / fatty acid binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Post-translational protein phosphorylation / cellular response to iron(III) ion / 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 / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / 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 / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / pyridoxal phosphate binding / positive regulation of protein binding / tertiary granule lumen / Platelet degranulation / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / blood microparticle / endosome membrane / immune response / copper ion binding / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å | ||||||
Authors | Schmidt, M.M. / Townson, S.A. / Andreucci, A. / Dombrowski, C. / Erbe, D.V. / King, B. / Kovalchin, J.T. / Masci, A. / Murillo, A. / Schirmer, E.B. ...Schmidt, M.M. / Townson, S.A. / Andreucci, A. / Dombrowski, C. / Erbe, D.V. / King, B. / Kovalchin, J.T. / Masci, A. / Murillo, A. / Schirmer, E.B. / Furfine, E.S. / Barnes, T.M. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Crystal structure of an HSA/FcRn complex reveals recycling by competitive mimicry of HSA ligands at a pH-dependent hydrophobic interface. Authors: Schmidt, M.M. / Townson, S.A. / Andreucci, A.J. / King, B.M. / Schirmer, E.B. / Murillo, A.J. / Dombrowski, C. / Tisdale, A.W. / Lowden, P.A. / Masci, A.L. / Kovalchin, J.T. / Erbe, D.V. / ...Authors: Schmidt, M.M. / Townson, S.A. / Andreucci, A.J. / King, B.M. / Schirmer, E.B. / Murillo, A.J. / Dombrowski, C. / Tisdale, A.W. / Lowden, P.A. / Masci, A.L. / Kovalchin, J.T. / Erbe, D.V. / Wittrup, K.D. / Furfine, E.S. / Barnes, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k71.cif.gz | 751.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k71.ent.gz | 643.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k71_validation.pdf.gz | 485 KB | Display | wwPDB validaton report |
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Full document | 4k71_full_validation.pdf.gz | 495.9 KB | Display | |
Data in XML | 4k71_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 4k71_validation.cif.gz | 86.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k71 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k71 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 66473.148 Da / Num. of mol.: 2 / 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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02768 #2: Protein | Mass: 30408.104 Da / Num. of mol.: 2 / Fragment: UNP residues 24-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P55899 #3: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P61769 #4: Chemical | ChemComp-SO4 / #5: 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: 3.07 Å3/Da / Density % sol: 60.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97872 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 16, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→108.29 Å / Num. obs: 103179 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2.4→2.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.67 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.4→108.29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 18.944 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.245 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.671 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→108.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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