+Open data
-Basic information
Entry | Database: PDB / ID: 6biv | |||||||||
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Title | HLA-DRB1 in complex with citrullinated LL37 peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis | |||||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / cytolysis / 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 / killing by host of symbiont cells / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...regulation of interleukin-4 production / regulation of interleukin-10 production / cytolysis / 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 / killing by host of symbiont cells / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / specific granule / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / cellular response to peptidoglycan / positive regulation of memory T cell differentiation / neutrophil activation / positive regulation of monocyte differentiation / CD4 receptor binding / cellular response to interleukin-6 / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / Antimicrobial peptides / polysaccharide binding / T-helper 1 type immune response / 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 / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / cellular response to interleukin-1 / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / innate immune response in mucosa / cell projection / lumenal side of endoplasmic reticulum membrane / lipopolysaccharide binding / protein tetramerization / 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 / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of angiogenesis / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / tertiary granule lumen / MHC class II protein complex binding / late endosome membrane / cellular response to tumor necrosis factor / T cell receptor signaling pathway / early endosome membrane / antibacterial humoral response / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / amyloid fibril formation / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 6biv.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6biv.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 6biv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6biv_validation.pdf.gz | 467.8 KB | Display | wwPDB validaton report |
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Full document | 6biv_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | 6biv_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6biv_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6biv ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6biv | HTTPS FTP |
-Related structure data
Related structure data | 6bijC 6bilC 6binC 6birC 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: 1476.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913*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: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 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: Jul 23, 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: 2.9→45.08 Å / Num. obs: 10253 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 47.37 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.06883 / Rpim(I) all: 0.108 / Rrim(I) all: 0.286 / Net I/σ(I): 7.5 / Num. measured all: 70429 / Scaling rejects: 34 | ||||||||||||||||||||||||
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: 2.9→45.076 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.91 Å2 / Biso mean: 43.2186 Å2 / Biso min: 21.69 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→45.076 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: 4 / % reflection obs: 100 %
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