+Open data
-Basic information
Entry | Database: PDB / ID: 6bil | |||||||||
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Title | HLA-DRB1 in complex with citrullinated fibrinogen peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis | |||||||||
Function / homology | Function and homology information induction of bacterial agglutination / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / fibrinogen complex / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...induction of bacterial agglutination / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / fibrinogen complex / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / Regulation of TLR by endogenous ligand / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / platelet alpha granule / blood coagulation, fibrin clot formation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / cellular response to leptin stimulus / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / intermediate filament / transport vesicle membrane / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / polysaccharide binding / T-helper 1 type immune response / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of peptide hormone secretion / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of vasoconstriction / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / cellular response to interleukin-1 / protein polymerization / PD-1 signaling / epidermis development / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of inflammatory response to antigenic stimulus / fibrinolysis / MHC class II antigen presentation / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Signaling by high-kinase activity BRAF mutants / response to calcium ion / MAP2K and MAPK activation / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / platelet aggregation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Downstream TCR signaling / Platelet degranulation / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / protein-folding chaperone binding / positive regulation of canonical NF-kappaB signal transduction / ER-Phagosome pathway / cell cortex Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 6bil.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bil.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bil_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 6bil_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 6bil_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 6bil_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6bil ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bil | HTTPS FTP |
-Related structure data
Related structure data | 6bijC 6binC 6birC 6bivC 6bixC 6biyC 6bizC 4mdiS C: citing same article (ref.) S: Starting model for refinement |
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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
#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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#2: 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 | ||
#3: Protein/peptide | Mass: 1292.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02675*PLUS | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 26% 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: Jun 26, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.4→39.14 Å / Num. obs: 19186 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.064 / Rrim(I) all: 0.172 / Net I/σ(I): 11.1 / Num. measured all: 136600 / Scaling rejects: 8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDI Resolution: 2.4→32.317 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.94 Å2 / Biso mean: 26.233 Å2 / Biso min: 8.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→32.317 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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