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Yorodumi- PDB-7q15: Crystal structure of FcRn and beta-2-microglobulin in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q15 | ||||||
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Title | Crystal structure of FcRn and beta-2-microglobulin in complex with IgG1-Fc-MST-HN (efgartigimod) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Neonatal Fc Receptor FcRn / FcRn / Fc / IgG1-Fc-MST-HN / efgartigimod / ARGX-113 / FcRn-binding protein | ||||||
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 / DAP12 interactions / negative regulation of receptor binding ...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 / DAP12 interactions / negative regulation of receptor binding / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / positive regulation of cellular senescence / peptide antigen binding / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / 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 / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å | ||||||
Authors | Pannecoucke, E. / Savvides, S.N. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: The Fab region of IgG impairs the internalization pathway of FcRn upon Fc engagement. Authors: Brinkhaus, M. / Pannecoucke, E. / van der Kooi, E.J. / Bentlage, A.E.H. / Derksen, N.I.L. / Andries, J. / Balbino, B. / Sips, M. / Ulrichts, P. / Verheesen, P. / de Haard, H. / Rispens, T. / ...Authors: Brinkhaus, M. / Pannecoucke, E. / van der Kooi, E.J. / Bentlage, A.E.H. / Derksen, N.I.L. / Andries, J. / Balbino, B. / Sips, M. / Ulrichts, P. / Verheesen, P. / de Haard, H. / Rispens, T. / Savvides, S.N. / Vidarsson, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q15.cif.gz | 450.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q15.ent.gz | 365.4 KB | Display | PDB format |
PDBx/mmJSON format | 7q15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q15_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7q15_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7q15_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 7q15_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/7q15 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q15 | HTTPS FTP |
-Related structure data
Related structure data | 7q3pC 1n0uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37225.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Variant (production host): MGAT-/- TR+ / References: UniProt: P55899 #2: Protein | Mass: 13732.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Variant (production host): MGAT-/- TR+ / References: UniProt: P61769 #3: Antibody | Mass: 25492.846 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Has ligand of interest | N | |
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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: 2.94 Å3/Da / Density % sol: 58.11 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Sodium Cacodylate pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.89 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 3.146→48.901 Å / Num. obs: 21510 / % possible obs: 90.4 % / Redundancy: 3.1 % / CC1/2: 0.942 / Rrim(I) all: 0.38 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 3.146→3.449 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1073 / CC1/2: 0.265 / Rrim(I) all: 0.0156 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N0U Resolution: 3.301→48.9 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.805 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.578
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Displacement parameters | Biso mean: 63.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.301→48.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.301→3.49 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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