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Open data
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Basic information
Entry | Database: PDB / ID: 2pxy | ||||||
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Title | Crystal structures of immune receptor complexes | ||||||
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![]() | IMMUNE SYSTEM / complex | ||||||
Function / homology | ![]() antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / T cell receptor complex / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / T cell receptor complex / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / cell surface receptor signaling pathway / lysosome / early endosome / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feng, D. / Bond, C.J. / Ely, L.K. / Garcia, K.C. | ||||||
![]() | ![]() Title: Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon'. Authors: Feng, D. / Bond, C.J. / Ely, L.K. / Maynard, J. / Garcia, K.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.7 KB | Display | ![]() |
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PDB format | ![]() | 110.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.7 KB | Display | ![]() |
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Full document | ![]() | 468.1 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-T cell receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 12537.667 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 12079.190 Da / Num. of mol.: 1 / Mutation: G17E,H47Y,I75T,L78S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-H-2 class II histocompatibility antigen, A-U ... , 2 types, 2 molecules CD
#3: Protein | Mass: 20771.111 Da / Num. of mol.: 1 / Fragment: extracellular alpha-1, extracellular alpha-2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 22566.240 Da / Num. of mol.: 1 / Fragment: extracellular beta-1, extracellular beta-2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 330 molecules P![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Protein/peptide | Mass: 1433.511 Da / Num. of mol.: 1 / Mutation: K4Y / Source method: obtained synthetically Details: Synthetic construct. The sequence can be naturally found in Mus musculus (Mouse) |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M succinic acid (pH7.0), 16% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47 Å / Num. all: 42263 / Num. obs: 42263 / Redundancy: 4.3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.2→2.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 37.2 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→47 Å
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