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Yorodumi- PDB-1frt: CRYSTAL STRUCTURE OF THE COMPLEX OF RAT NEONATAL FC RECEPTOR WITH FC -
+Open data
-Basic information
Entry | Database: PDB / ID: 1frt | |||||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF RAT NEONATAL FC RECEPTOR WITH FC | |||||||||
Components |
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Keywords | COMPLEX (RECEPTOR/IMMUNOGLOBULIN) / COMPLEX (RECEPTOR-IMMUNOGLOBULIN) / COMPLEX (RECEPTOR-IMMUNOGLOBULIN) complex | |||||||||
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 / cellular response to iron ion / 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 / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / response to xenobiotic stimulus / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 4.5 Å | |||||||||
Authors | Burmeister, W.P. / Bjorkman, P.J. | |||||||||
Citation | Journal: Nature / Year: 1994 Title: Crystal structure of the complex of rat neonatal Fc receptor with Fc. Authors: Burmeister, W.P. / Huber, A.H. / Bjorkman, P.J. #1: Journal: Nature / Year: 1994 Title: Crystal Structure at 2.2 Angstroms Resolution of the Mhc-Related Neonatal Fc Receptor Authors: Burmeister, W.P. / Gastinel, L.N. / Simister, N.E. / Blum, M.L. / Bjorkman, P.J. #2: Journal: Immunity / Year: 1994 Title: Investigation of the Interaction between the Class I Mhc-Related Fc Receptor and its Immunoglobulin G Ligand Authors: Raghavan, M. / Chen, M.Y. / Gastinel, L.N. / Bjorkman, P.J. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Stoichiometry of Binding of a Complex between a Rat Intestinal Fc Receptor and Fc Authors: Huber, A.H. / Kelly, R.F. / Gastinel, L.N. / Bjorkman, P.J. #4: Journal: Biochemistry / Year: 1981 Title: Crystallographic Refinement and Atomic Models of a Human Fc Fragment and its Complex with Fragment B of Protein a from Staphylococcus Aureus at 2.9-And 2.8-Angstroms Resolution Authors: Deisenhofer, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1frt.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1frt.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 1frt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1frt_validation.pdf.gz | 567.5 KB | Display | wwPDB validaton report |
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Full document | 1frt_full_validation.pdf.gz | 596.4 KB | Display | |
Data in XML | 1frt_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1frt_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1frt ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1frt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 207 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO C 374 | ||||||||
Details | MTRIX THE INFORMATION PRESENTED ON SYMMETRY RECORDS BELOW DESCRIBE TRANSFORMATIONS TO GENERATE CRYSTALLOGRAPHIC RELATIONSHIPS AS DESCRIBED IN THE STATEMENT THAT FOLLOWS EACH SYMMETRY OPERATOR. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD S1 C 1 - C 443 ? 1 - ? 443 THIS TRANSFORMATION GENERATES THE SECOND CHAIN OF THE FC MOLECULE. IF THE SAME OPERATION IS ALSO APPLIED TO THE FCRN MOLECULE, THE "STANDING UP" FCRNFC COMPLEX DISCUSSED IN THE ACCOMPANYING PAPER IS GENERATED. S2 A 1 - A 405 ? 1 - ? 405 S2 B 1 - B 99 ? 1 - ? 99 THIS TRANSFORMATION GENERATES THE SECOND SUBUNIT FOR THE "LYING DOWN" FC RECEPTOR DIMER PRESENTED IN THE ACCOMPANYING PAPER. SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 -1.000000 0.000000 145.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 108.25000 SYMMETRY1 2 -1.000000 0.000000 0.000000 250.00000 SYMMETRY2 2 0.000000 -1.000000 0.000000 72.50000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 |
-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 30322.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BETA-2-MICROGLOBULIN / Organ: SERUM (MIXTURE OF SEVERAL SUBTYPES) / Plasmid: PBJ5-GS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P13599 |
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#2: Protein | Mass: 11652.282 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BETA-2-MICROGLOBULIN / Organ: SERUM (MIXTURE OF SEVERAL SUBTYPES) / Plasmid: PBJ5-GS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P07151 |
#3: Protein | Mass: 23422.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BETA-2-MICROGLOBULIN / Organ: SERUM (MIXTURE OF SEVERAL SUBTYPES) / Plasmid: PBJ5-GS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: GenBank: 243866 |
-Sugars , 3 types, 3 molecules
#4: 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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#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-(1-6)-[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 |
#6: Sugar | ChemComp-NAG / |
-Details
Sequence details | THERE ARE A NUMBER OF CLOSE CONTACTS BETWEEN ATOMS IN THIS THIS MOLECULE AND IN SYMMETRY-RELATED MOLECULES. |
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Source details | SOURCE 1 MOLECULE_NAME: FC (IGG) RECEPTOR, NEONATAL (FCRN) THE CELL LINE SECRETES A SOLUBLE FCRN ...SOURCE 1 MOLECULE_NAME: FC (IGG) RECEPTOR, NEONATAL (FCRN) THE CELL LINE SECRETES A SOLUBLE FCRN HETERODIME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 6.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 8527 / % possible obs: 67 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 4.5 Å / Lowest resolution: 25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.125 |
Reflection shell | *PLUS Highest resolution: 4.5 Å / Lowest resolution: 4.7 Å / % possible obs: 23 % / Rmerge(I) obs: 0.289 |
-Processing
Software |
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Refinement | Resolution: 4.5→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 199 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→20 Å
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