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Yorodumi- PDB-1i1a: CRYSTAL STRUCTURE OF THE NEONATAL FC RECEPTOR COMPLEXED WITH A HE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i1a | |||||||||
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Title | CRYSTAL STRUCTURE OF THE NEONATAL FC RECEPTOR COMPLEXED WITH A HETERODIMERIC FC | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I fold / Ig constant domains | |||||||||
Function / homology | Function and homology information 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 / Neutrophil degranulation / humoral immune response ...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 / Neutrophil degranulation / humoral immune response / beta-2-microglobulin binding / response to cadmium ion / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / cellular response to iron ion / antigen binding / 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 / 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 / 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 / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / blood microparticle / endosome membrane / response to xenobiotic stimulus / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
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: 2001 Title: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 |
-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.) Rattus norvegicus (Norway rat) / Plasmid: PBJ-5GS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P13599 |
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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.) Rattus norvegicus (Norway rat) / Plasmid: PBJ-5GS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P07151 |
-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.) Rattus norvegicus (Norway rat) / Plasmid: PBJ-5GS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P20760 |
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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.) Rattus norvegicus (Norway rat) / Plasmid: PBJ-5GS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P20760 |
-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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-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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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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