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Open data
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Basic information
Entry | Database: PDB / ID: 6bir | |||||||||
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Title | HLA-DRB1 in complex with citrullinated Vimentin peptide | |||||||||
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![]() | IMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis | |||||||||
Function / homology | ![]() lens fiber cell development / keratin filament binding / intermediate filament organization / 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 ...lens fiber cell development / keratin filament binding / intermediate filament organization / 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 / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / structural constituent of eye lens / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / Striated Muscle Contraction / inflammatory response to antigenic stimulus / positive regulation of kinase activity / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / cell leading edge / 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 / Bergmann glial cell differentiation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / positive regulation of collagen biosynthetic process / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / regulation of mRNA stability / MHC class II antigen presentation / phagocytic vesicle / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / nuclear matrix / cellular response to type II interferon / Aggrephagy / peptide antigen assembly with MHC class II protein complex / Chaperone Mediated Autophagy / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peroxisome / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / neuron projection development / Interferon gamma signaling / positive regulation of immune response / double-stranded RNA binding / Downstream TCR signaling / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / membrane => GO:0016020 / molecular adaptor activity / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / cytoskeleton / endosome membrane / positive regulation of protein phosphorylation / immune response / protein domain specific binding / lysosomal membrane / external side of plasma membrane / axon Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ting, Y.T. / Scally, S.W. / Rossjohn, J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.6 KB | Display | ![]() |
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PDB format | ![]() | 70.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467 KB | Display | ![]() |
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Full document | ![]() | 468.3 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bijC ![]() 6bilC ![]() 6binC ![]() 6bivC ![]() 6bixC ![]() 6biyC ![]() 6bizC ![]() 4mdiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() | ||
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#2: Protein | Mass: 23224.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Protein/peptide | Mass: 1462.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 6.5 Details: Imidazole/MES pH 6.5, 0.01 M ammonium sulfate, 0.01 M di-sodium hydrogen phosphate, 0.01 M sodium nitrate, 12.5% 2-methyl-2,4-pentanediol (MPD), 14% PEG3350, 12.5% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→39.345 Å / Num. obs: 21534 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.61 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.072 / Rrim(I) all: 0.19 / Net I/σ(I): 9.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MDI Resolution: 2.3→39.344 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.28 Å2 / Biso mean: 25.5611 Å2 / Biso min: 9.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→39.344 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: 8
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