+Open data
-Basic information
Entry | Database: PDB / ID: 6bin | ||||||||||||
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Title | HLA-DRB1 in complex with Type II collagen peptide | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis | ||||||||||||
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 / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / 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 / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / regulation of interleukin-4 production / Extracellular matrix organization / notochord development / limb bud formation / regulation of interleukin-10 production / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / 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 / 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 / positive regulation of kinase activity / inflammatory response to antigenic stimulus / collagen fibril organization / cartilage development / proteoglycan binding / transport vesicle membrane / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / intermediate filament / inner ear morphogenesis / polysaccharide binding / T-helper 1 type immune response / 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 / 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 / heart morphogenesis / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / extrinsic apoptotic signaling pathway in absence of ligand / MHC class II antigen presentation / visual perception / trans-Golgi network membrane / central nervous system development / skeletal 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 / 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 / positive regulation of canonical NF-kappaB signal transduction Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50000845062 Å | ||||||||||||
Authors | Ting, Y.T. / Scally, S.W. / Rossjohn, J. | ||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis. Authors: Ting, Y.T. / Petersen, J. / Ramarathinam, S.H. / Scally, S.W. / Loh, K.L. / Thomas, R. / Suri, A. / Baker, D.G. / Purcell, A.W. / Reid, H.H. / Rossjohn, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bin.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bin.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 6bin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6bin ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bin | HTTPS FTP |
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-Related structure data
Related structure data | 6bijC 6bilC 6birC 6bivC 6bixC 6biyC 6bizC 4mdiS 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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-Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21919.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P01903 |
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#3: Protein | Mass: 23224.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P13760, UniProt: P01911*PLUS |
-Protein/peptide / Non-polymers , 2 types, 114 molecules C
#2: Protein/peptide | Mass: 1438.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P02458*PLUS |
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#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 3 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 22-28% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.47 Å / Num. obs: 16976 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 27.4753195141 Å2 / CC1/2: 0.983 / Net I/σ(I): 7.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDI Resolution: 2.50000845062→39.4694272359 Å / SU ML: 0.301740799289 / Cross valid method: FREE R-VALUE / σ(F): 1.33605370712 / Phase error: 22.6576261995 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7319790708 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.50000845062→39.4694272359 Å
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Refine LS restraints |
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LS refinement shell |
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