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Open data
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Basic information
| Entry | Database: PDB / ID: 2wbj | |||||||||
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| Title | TCR complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / TRANSMEMBRANE / IMMUNE RESPONSE / T CELL RECEPTOR / MHC II / MEMBRANE / RECEPTOR / MOLECULAR MIMICRY / MULTIPLE SCLEROSIS / AUTOIMMUNITY / GLYCOPROTEIN / MHC CLASS II | |||||||||
| Function / homology | Function and homology informationregulation of interleukin-4 production / regulation of interleukin-10 production / autolysosome membrane / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / 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 T cell mediated immune response to tumor cell ...regulation of interleukin-4 production / regulation of interleukin-10 production / autolysosome membrane / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / 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 T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / T-helper 1 type immune response / intermediate filament / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / Generation of second messenger molecules / macrophage differentiation / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / negative regulation of T cell proliferation / T cell receptor binding / MHC class II antigen presentation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / ER to Golgi transport vesicle membrane / clathrin-coated endocytic vesicle membrane / negative regulation of inflammatory response to antigenic stimulus / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / structural constituent of cytoskeleton / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / cognition / positive regulation of T cell activation / Interferon gamma signaling / endocytic vesicle membrane / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / adaptive immune response / lysosome / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / cell surface / signal transduction / : / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
| Biological species | HOMO SAPIENS (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Harkiolaki, M. / Holmes, S.L. / Svendsen, P. / Gregersen, J.W. / Jensen, L.T. / McMahon, R. / Friese, M.A. / van Boxel, G. / Etzensperger, R. / Tzartos, J.S. ...Harkiolaki, M. / Holmes, S.L. / Svendsen, P. / Gregersen, J.W. / Jensen, L.T. / McMahon, R. / Friese, M.A. / van Boxel, G. / Etzensperger, R. / Tzartos, J.S. / Kranc, K. / Sainsbury, S. / Harlos, K. / Mellins, E.D. / Palace, J. / Esiri, M.M. / van der Merwe, P.A. / Jones, E.Y. / Fugger, L. | |||||||||
Citation | Journal: Immunity / Year: 2009Title: T Cell-Mediated Autoimmune Disease due to Low-Affinity Crossreactivity to Common Microbial Peptides. Authors: Harkiolaki, M. / Holmes, S.L. / Svendsen, P. / Gregersen, J.W. / Jensen, L.T. / Mcmahon, R. / Friese, M.A. / Van Boxel, G. / Etzensperger, R. / Tzartos, J.S. / Kranc, K. / Sainsbury, S. / ...Authors: Harkiolaki, M. / Holmes, S.L. / Svendsen, P. / Gregersen, J.W. / Jensen, L.T. / Mcmahon, R. / Friese, M.A. / Van Boxel, G. / Etzensperger, R. / Tzartos, J.S. / Kranc, K. / Sainsbury, S. / Harlos, K. / Mellins, E.D. / Palace, J. / Esiri, M.M. / Van Der Merwe, P.A. / Jones, E.Y. / Fugger, L. | |||||||||
| History |
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| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2wbj.cif.gz | 338.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2wbj.ent.gz | 271.4 KB | Display | PDB format |
| PDBx/mmJSON format | 2wbj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbj ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbj | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 1ymmS S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, ... , 2 types, 4 molecules AEBF
| #1: Protein | Mass: 22436.246 Da / Num. of mol.: 2 / Fragment: MHC CLASS II, RESIDUES 26-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 CELLS / Production host: ![]() #2: Protein | Mass: 23205.834 Da / Num. of mol.: 2 / Fragment: MHC CLASS II, RESIDUES 29-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 CELLS / Production host: ![]() |
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-Antibody / Protein / Non-polymers , 3 types, 7 molecules CGDH

| #3: Antibody | Mass: 24474.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: E. COLI ENGA PEPTIDE COVALENTLY BOUND / Source: (gene. exp.) HOMO SAPIENS (human) / Description: PATIENT DERIVED SEQUENCE / Plasmid: PET22 / Production host: ![]() #4: Protein | Mass: 30826.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: E. COLI ENGA PEPTIDE COVALENTLY BOUND / Source: (gene. exp.) HOMO SAPIENS (human) / Description: PATIENT DERIVED SEQUENCE / Plasmid: PET22 / Production host: ![]() #7: Chemical | |
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-Sugars , 2 types, 5 molecules 
| #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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| #6: Sugar | ChemComp-NAG / |
-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.3 % / Description: NONE |
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| Crystal grow | pH: 6.3 Details: 0.2 M LISO4, 0.8 M K2HPO4, 1.2 M NAH2PO4, 0.1 M CAPS PH 10.5, 8 % 1,1,1,3,3, 3-HEXAFLUORO-2-PROPANOL |
-Data collection
| Diffraction | Mean temperature: 77 K |
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| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
| Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
| Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
| Reflection | Resolution: 3.15→30 Å / Num. obs: 45361 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 16.9 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 10.3 |
| Reflection shell | Resolution: 3.15→3.26 Å / Redundancy: 16.6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1YMM Resolution: 3→105.41 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.864 / SU B: 45.999 / SU ML: 0.408 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 64.111 Å2
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| Refinement step | Cycle: LAST / Resolution: 3→105.41 Å
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| Refine LS restraints |
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About Yorodumi




HOMO SAPIENS (human)
X-RAY DIFFRACTION
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