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Open data
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Basic information
Entry | Database: PDB / ID: 3qib | ||||||
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Title | Crystal structure of the 2B4 TCR in complex with MCC/I-Ek | ||||||
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![]() | IMMUNE SYSTEM / Ig domain | ||||||
Function / homology | ![]() Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / alpha-beta T cell receptor complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Translocation of ZAP-70 to Immunological synapse ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / alpha-beta T cell receptor complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / : / PD-1 signaling / response to bacterium / mitochondrial intermembrane space / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / adaptive immune response / electron transfer activity / lysosomal membrane / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ely, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C. | ||||||
![]() | ![]() Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k). Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M. | ||||||
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 | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 540.5 KB | Display | ![]() |
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Full document | ![]() | 571.2 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 47.6 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
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 22491.221 Da / Num. of mol.: 1 / Fragment: unp residues 26-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 23344.934 Da / Num. of mol.: 1 / Fragment: unp residues 29-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 22807.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 30288.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules P
#5: Protein/peptide | Mass: 1393.628 Da / Num. of mol.: 1 / Fragment: unp residues 97-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 5 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/FUC.gif)
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![](data/chem/img/FUC.gif)
![](data/chem/img/BMA.gif)
#6: Sugar | #7: Sugar | #9: Sugar | ChemComp-BMA / | |
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-Non-polymers , 2 types, 113 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-PEG / #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 68.99 % |
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Crystal grow | Temperature: 295 K / pH: 6.2 Details: 50% PEG200, 0.2 M sodium chloride, 0.1 M sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2009 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 43820 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.63 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→34.97 Å
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Refine LS restraints |
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LS refinement shell |
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