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Yorodumi- PDB-2fse: Crystallographic structure of a rheumatoid arthritis MHC suscepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fse | ||||||
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Title | Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1 (DRB1*0101), complexed with the immunodominant determinant of human type II collagen | ||||||
Components |
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Keywords | IMMUNE SYSTEM / STRUCTURAL PROTEIN / rheumatoid arthritis / HLA-DR1 / collagen type II / antigen presentation | ||||||
Function / homology | Function and homology information collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / regulation of interleukin-4 production ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / regulation of interleukin-4 production / Extracellular matrix organization / cartilage development involved in endochondral bone morphogenesis / notochord development / regulation of interleukin-10 production / limb bud formation / Collagen biosynthesis and modifying enzymes / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / tissue homeostasis / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / Signaling by PDGF / cellular response to BMP stimulus / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / endochondral ossification / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / NCAM1 interactions / positive regulation of kinase activity / inflammatory response to antigenic stimulus / collagen fibril organization / cartilage development / intermediate filament / proteoglycan binding / transport vesicle membrane / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / inner ear morphogenesis / T-helper 1 type immune response / polysaccharide binding / cartilage condensation / roof of mouth development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Collagen degradation / Generation of second messenger molecules / Non-integrin membrane-ECM interactions / immunological synapse / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / PD-1 signaling / ECM proteoglycans / epidermis development / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / negative regulation of inflammatory response to antigenic stimulus / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of T cell proliferation / MHC class II antigen presentation / visual perception / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / central nervous system development / skeletal system development / lumenal side of endoplasmic reticulum membrane / sensory perception of sound / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / 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 / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / regulation of gene expression / collagen-containing extracellular matrix Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Ivey, R.A. / Rosloniec, E.F. / Whittington, K.B. / Kang, A.H. / Park, H.W. | ||||||
Citation | Journal: J.Immunol. / Year: 2006 Title: Crystallographic Structure of a Rheumatoid Arthritis MHC Susceptibility Allele, HLA-DR1 (DRB1*0101), Complexed with the Immunodominant Determinant of Human Type II Collagen. Authors: Rosloniec, E.F. / Ivey, R.A. / Whittington, K.B. / Kang, A.H. / Park, H.W. | ||||||
History |
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Remark 999 | SEQUENCE THERE WAS NO SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING FOR THE MHC CHAINS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fse.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fse.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/2fse ftp://data.pdbj.org/pub/pdb/validation_reports/fs/2fse | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20711.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chains A and C form a chimera with chains B and D, respectively Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903 #2: Protein | Mass: 21909.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chains B and D form a chimera with chains A and C, respectively Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04229, UniProt: P01911*PLUS #3: Protein/peptide | Mass: 1360.471 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL2A1 / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P02458 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% polyethylene glycol 3,350 and 200 mM ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→91.287 Å / Num. all: 21330 / Num. obs: 20446 / % possible obs: 82.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Limit h max: 19 / Limit h min: 0 / Limit k max: 35 / Limit k min: 0 / Limit l max: 55 / Limit l min: 0 / Rsym value: 0.099 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2046 / Rsym value: 0.382 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / σ(F): 1936
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Solvent computation | Bsol: 15.01 Å2 | ||||||||||||||||
Displacement parameters | Biso mean: 26.877 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Xplor file |
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