+Open data
-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 information 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 / 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 ...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 / 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 / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / 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 / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / 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 / 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 / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of protein phosphorylation / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / 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: 2009 Title: 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wbj.cif.gz | 338.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbj.ent.gz | 271.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wbj_validation.pdf.gz | 891.2 KB | Display | wwPDB validaton report |
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Full document | 2wbj_full_validation.pdf.gz | 924.8 KB | Display | |
Data in XML | 2wbj_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 2wbj_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbj ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbj | HTTPS FTP |
-Related structure data
Related structure data | 1ymmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P01903 #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: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P01911 |
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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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) #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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) #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 / |
-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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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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