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Yorodumi- PDB-5bjt: Crystal structure of human FcRn with a peptide inhibitor at multi... -
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-Basic information
Entry | Database: PDB / ID: 5bjt | ||||||
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Title | Crystal structure of human FcRn with a peptide inhibitor at multiple sites | ||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / immunoglobulin binding protein / cell membrane / disulfide bond / glycoprotein / IgG-binding protein / immunoglobulin domain / receptor / transmembrane / amyloid / amyloidosis / disease mutation / glycation / immune response / MHC I / pyrrolidone carboxylic acid / secreted / IMMUNE SYSTEM-INHIBITOR complex | ||||||
Function / homology | Function and homology information IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / 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 / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / 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 / endosome membrane / immune response / 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 / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Nienaber, V. / Badger, J. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Hepatic FcRn regulates albumin homeostasis and susceptibility to liver injury. Authors: Pyzik, M. / Rath, T. / Kuo, T.T. / Win, S. / Baker, K. / Hubbard, J.J. / Grenha, R. / Gandhi, A. / Kramer, T.D. / Mezo, A.R. / Taylor, Z.S. / McDonnell, K. / Nienaber, V. / Andersen, J.T. / ...Authors: Pyzik, M. / Rath, T. / Kuo, T.T. / Win, S. / Baker, K. / Hubbard, J.J. / Grenha, R. / Gandhi, A. / Kramer, T.D. / Mezo, A.R. / Taylor, Z.S. / McDonnell, K. / Nienaber, V. / Andersen, J.T. / Mizoguchi, A. / Blumberg, L. / Purohit, S. / Jones, S.D. / Christianson, G. / Lencer, W.I. / Sandlie, I. / Kaplowitz, N. / Roopenian, D.C. / Blumberg, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bjt.cif.gz | 299.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bjt.ent.gz | 235.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/5bjt ftp://data.pdbj.org/pub/pdb/validation_reports/bj/5bjt | HTTPS FTP |
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-Related structure data
Related structure data | 3m17S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 29720.383 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 24-290) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P55899 #2: Protein | Mass: 11748.160 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61769 #3: Protein/peptide | Mass: 2158.483 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 3.13 Å3/Da / Density % sol: 60.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 1.6 M ammonium sulfate, 20% glycerol, 0.8 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2008 |
Radiation | Monochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 37736 / % possible obs: 99.9 % / Observed criterion σ(I): -4 / Redundancy: 5.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3M17 Resolution: 3.2→49.27 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.79 / SU B: 29.352 / SU ML: 0.52 / Cross valid method: THROUGHOUT / ESU R Free: 0.624
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.17 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→49.27 Å
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Refine LS restraints |
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