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- PDB-2fse: Crystallographic structure of a rheumatoid arthritis MHC suscepti... -
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Open data
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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 | ||||||
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![]() | IMMUNE SYSTEM / STRUCTURAL PROTEIN / rheumatoid arthritis / HLA-DR1 / collagen type II / antigen presentation | ||||||
Function / homology | ![]() collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / regulation of interleukin-4 production / Extracellular matrix organization ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / regulation of interleukin-4 production / Extracellular matrix organization / notochord development / limb bud formation / regulation of interleukin-10 production / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / tissue homeostasis / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / cellular response to BMP stimulus / Signaling by PDGF / 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 / inflammatory response to antigenic stimulus / positive regulation of kinase activity / collagen fibril organization / cartilage development / proteoglycan binding / transport vesicle membrane / intermediate filament / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / polysaccharide binding / T-helper 1 type immune response / cartilage condensation / inner ear morphogenesis / 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 / immunological synapse / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / PD-1 signaling / epidermis development / Integrin cell surface interactions / chondrocyte differentiation / T cell receptor binding / heart morphogenesis / detection of bacterium / negative regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of inflammatory response to antigenic stimulus / visual perception / MHC class II antigen presentation / trans-Golgi network membrane / skeletal system development / central nervous system development / lumenal side of endoplasmic reticulum membrane / protein tetramerization / sensory perception of sound / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / regulation of gene expression / positive regulation of canonical NF-kappaB signal transduction Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ivey, R.A. / Rosloniec, E.F. / Whittington, K.B. / Kang, A.H. / Park, H.W. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.9 KB | Display | ![]() |
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PDB format | ![]() | 130.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.9 KB | Display | ![]() |
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Full document | ![]() | 499.9 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1360.471 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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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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