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Open data
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Basic information
Entry | Database: PDB / ID: 3qiw | ||||||
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Title | Crystal structure of the 226 TCR in complex with MCC-p5E/I-Ek | ||||||
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![]() | IMMUNE SYSTEM / immunoglobulin domain / T cell receptor / MHC molecule | ||||||
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 / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space ...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 / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / electron transfer activity / lysosomal membrane / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kruse, A.C. / 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 | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 133.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.4 KB | Display | ![]() |
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Full document | ![]() | 502.4 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qibC ![]() 3qiuSC ![]() 3qjfC ![]() 3qjhC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 22361.051 Da / Num. of mol.: 1 / Fragment: unp residues 26-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 22972.594 Da / Num. of mol.: 1 / Fragment: unp residues 29-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 22822.301 Da / Num. of mol.: 1 / Fragment: unp residues 97-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 27613.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide / Sugars , 2 types, 3 molecules E![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#5: Protein/peptide | Mass: 1393.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#6: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.24 % |
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Crystal grow | Temperature: 295 K / pH: 6.5 Details: 15-20% PEG5000 MME, Bis tris, VAPOR DIFFUSION, temperature 295K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→45 Å / Num. obs: 16259 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.345 / % possible all: 99.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3QIU Resolution: 3.3→36.69 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.44 / σ(F): 1.36 / Phase error: 28.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.48 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.75 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→36.69 Å
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Refine LS restraints |
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LS refinement shell |
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