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- PDB-2iam: Structural basis for recognition of mutant self by a tumor-specif... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iam | ||||||
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Title | Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR | ||||||
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![]() | IMMUNE SYSTEM / major histocompatibility complex / T cell receptor / T cell stimulation / melanoma / tumor antigen | ||||||
Function / homology | ![]() methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / 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 ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / 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 / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / CD4 receptor binding / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / inflammatory response to antigenic stimulus / positive regulation of kinase activity / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / glycerol catabolic process / Glycolysis / transport vesicle membrane / intermediate filament / 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 / alpha-beta T cell activation / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / complement activation, classical pathway / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / glycolytic process / protein tetramerization / antigen binding / response to bacterium / 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 / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / antibacterial humoral response / 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 / blood microparticle / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Deng, L. / Langley, R.J. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor Authors: Deng, L. / Langley, R.J. / Brown, P.H. / Xu, G. / Teng, L. / Wang, Q. / Gonzales, M.I. / Callender, G.G. / Nishimura, M.I. / Topalian, S.L. / Mariuzza, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.2 KB | Display | ![]() |
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PDB format | ![]() | 137.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 487 KB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ialC ![]() 2ianC ![]() 1fytS ![]() 1ialS C: citing same article ( 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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Unit cell |
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Details | Each asymmetric unit contains one biological unit. |
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Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21155.904 Da / Num. of mol.: 1 / Fragment: residues 1-182 (26-207) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: residues 1-190 (30-219) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-CD4+ T cell receptor E8 ... , 2 types, 2 molecules CD
#4: Protein | Mass: 22399.682 Da / Num. of mol.: 1 / Mutation: T156C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 27088.197 Da / Num. of mol.: 1 / Mutation: S167C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 41 molecules P![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1481.713 Da / Num. of mol.: 1 / Fragment: residues 23-37 (22-36) / Mutation: T28I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 26581 / % possible obs: 92.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.8→2.94 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3 / Num. unique all: 5639 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FYT, 1IAL Resolution: 2.8→41.91 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 25.523 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.747 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 62.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→41.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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