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- PDB-5jlz: Crystal structure of HLA-DRB1*04:01 in complex with modified alph... -
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Basic information
Entry | Database: PDB / ID: 5jlz | |||||||||
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Title | Crystal structure of HLA-DRB1*04:01 in complex with modified alpha-enolase peptide 26-40 with citrulline at the position 32 | |||||||||
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![]() | IMMUNE SYSTEM / HLA / autoimmune desease / rheumatoid arthritis / MHC class II / citrulline | |||||||||
Function / homology | ![]() negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / regulation of interleukin-4 production / regulation of interleukin-10 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / myeloid dendritic cell antigen processing and presentation ...negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / regulation of interleukin-4 production / regulation of interleukin-10 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 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 / positive regulation of CD4-positive, alpha-beta T cell activation / 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 / Gluconeogenesis / inflammatory response to antigenic stimulus / nuclear outer membrane / positive regulation of kinase activity / M band / canonical glycolysis / Glycolysis / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / positive regulation of ATP biosynthetic process / 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 / 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 / transcription corepressor binding / trans-Golgi network membrane / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / glycolytic process / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / clathrin-coated endocytic vesicle membrane / response to virus / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / negative regulation of cell growth / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / transcription corepressor activity / 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 / GTPase binding / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / cell cortex / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / cadherin binding / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / magnesium ion binding / signal transduction / protein homodimerization activity / RNA binding / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dubnovitsky, A. / Kozhukh, G. / Sandalova, T. / Achour, A. | |||||||||
![]() | ![]() Title: Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted alpha-Enolase T Cell Epitope in Rheumatoid Arthritis. Authors: Gerstner, C. / Dubnovitsky, A. / Sandin, C. / Kozhukh, G. / Uchtenhagen, H. / James, E.A. / Ronnelid, J. / Ytterberg, A.J. / Pieper, J. / Reed, E. / Tandre, C. / Rieck, M. / Zubarev, R.A. / ...Authors: Gerstner, C. / Dubnovitsky, A. / Sandin, C. / Kozhukh, G. / Uchtenhagen, H. / James, E.A. / Ronnelid, J. / Ytterberg, A.J. / Pieper, J. / Reed, E. / Tandre, C. / Rieck, M. / Zubarev, R.A. / Ronnblom, L. / Sandalova, T. / Buckner, J.H. / Achour, A. / Malmstrom, V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.4 KB | Display | ![]() |
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PDB format | ![]() | 272.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 485.5 KB | Display | ![]() |
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Full document | ![]() | 494.7 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5laxC ![]() 4mcyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 21911.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Extracellular Domain, UNP residues 26-206 / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 23102.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Extracellular Domain, UNP residues 30-219 / Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1450.617 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Post-translational modification of Arg32 of human alpha-enolase Source: (synth.) ![]() #4: Chemical | ChemComp-MLA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1M sodium malonate, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→47.76 Å / Num. obs: 51357 / % possible obs: 99.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.99→2.05 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.9 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MCY Resolution: 1.99→47.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.329 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.751 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→47.76 Å
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Refine LS restraints |
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