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Yorodumi- PDB-1i1a: CRYSTAL STRUCTURE OF THE NEONATAL FC RECEPTOR COMPLEXED WITH A HE... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 1i1a | |||||||||
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| Title | CRYSTAL STRUCTURE OF THE NEONATAL FC RECEPTOR COMPLEXED WITH A HETERODIMERIC FC | |||||||||
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Keywords | IMMUNE SYSTEM / MHC class I fold / Ig constant domains | |||||||||
| Function / homology | Function and homology informationEndosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / IgG receptor activity / IgG binding / immunoglobulin receptor binding / immunoglobulin complex, circulating ...Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / IgG receptor activity / IgG binding / immunoglobulin receptor binding / immunoglobulin complex, circulating / Neutrophil degranulation / beta-2-microglobulin binding / humoral immune response / complement activation, classical pathway / response to cadmium ion / antigen binding / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / response to xenobiotic stimulus / lysosomal membrane / external side of plasma membrane / structural molecule activity / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Martin, W.L. / West Jr., A.P. / Gan, L. / Bjorkman, P.J. | |||||||||
Citation | Journal: Mol.Cell / Year: 2001Title: Crystal structure at 2.8 A of an FcRn/heterodimeric Fc complex: mechanism of pH-dependent binding. Authors: Martin, W.L. / West Jr., A.P. / Gan, L. / Bjorkman, P.J. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 1i1a.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb1i1a.ent.gz | 140.6 KB | Display | PDB format |
| PDBx/mmJSON format | 1i1a.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 1i1a_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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| Full document | 1i1a_full_validation.pdf.gz | 1.7 MB | Display | |
| Data in XML | 1i1a_validation.xml.gz | 35.5 KB | Display | |
| Data in CIF | 1i1a_validation.cif.gz | 47.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1a ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1a | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 1i1cC ![]() 1fc1S ![]() 3fruS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Details | The glycosylated heterodimer is the biological unit. The cysteines attached to cysteines 48 and 226 are the result of long term storage in the growth media. / The biological unit is a glycosylated homodimer. One of the two amino acid chains has been mutated as noted making the biological unit in this structure a heterodimer |
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Components
-Protein , 2 types, 2 molecules AB
| #1: Protein | Mass: 30322.887 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #2: Protein | Mass: 11652.282 Da / Num. of mol.: 1 / Fragment: FC FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-IG GAMMA-2A CHAIN C ... , 2 types, 2 molecules CD
| #3: Protein | Mass: 25248.506 Da / Num. of mol.: 1 / Fragment: WILD-TYPE FC FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #4: Protein | Mass: 26650.855 Da / Num. of mol.: 1 / Fragment: NON-FCRN-BINDING FC FRAGMENT / Mutation: T252G, I253G, T254G, H310E, H433E, H435E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 5 types, 6 molecules 
| #5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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| #6: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-alpha-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 |
| #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #8: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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 Source method: isolated from a genetically manipulated source |
| #9: Sugar |
-Non-polymers , 2 types, 8 molecules 


| #10: Chemical | | #11: Water | ChemComp-HOH / | |
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-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: 2.65 Å3/Da / Density % sol: 53.66 % | ||||||||||||||||||||||||||||||
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| Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PEG 8000, Ammonium Acetate, Sodium Acetate, Sodium cacodylate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
| Crystal grow | *PLUS pH: 4.5 | ||||||||||||||||||||||||||||||
| Components of the solutions | *PLUS
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-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
| Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 1999 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 2.8→20 Å / Num. all: 25005 / Num. obs: 25005 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.099 / Net I/σ(I): 18.9 |
| Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / Num. unique all: 2234 / Rsym value: 0.284 / % possible all: 89.6 |
| Reflection shell | *PLUS % possible obs: 89.6 % |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: pdb entry 3fru, pdb entry 1fc1 Resolution: 2.8→19.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1843766.66 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0
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| Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.3969 Å2 / ksol: 0.275823 e/Å3 | ||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 78.2 Å2
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| Refine analyze |
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| Refinement step | Cycle: LAST / Resolution: 2.8→19.95 Å
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| Refine LS restraints |
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| Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||
| LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
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| Xplor file |
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| Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
| Refine LS restraints | *PLUS
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