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- PDB-1kt2: CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kt2 | |||||||||
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Title | CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTOCHROME C PEPTIDE | |||||||||
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![]() | IMMUNE SYSTEM / Protein-peptide complex / T cell receptor / antigen presentation / cytochrome | |||||||||
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 / immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding ...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 / immunoglobulin mediated immune response / 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 / lysosome / lysosomal membrane / external side of plasma membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fremont, D.H. / Dai, S. / Chiang, H. / Crawford, F. / Marrack, P. / Kappler, J. | |||||||||
![]() | ![]() Title: Structural basis of cytochrome c presentation by IE(k). Authors: Fremont, D.H. / Dai, S. / Chiang, H. / Crawford, F. / Marrack, P. / Kappler, J. | |||||||||
History |
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Remark 999 | SEQUENCE RESIDUE 202 OF CHAINS A,C IS IN CONFLICT IN SWISSPROT ENTRY P01904. IT CAN BE EITHER THR OR HIS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.6 KB | Display | ![]() |
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PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.9 KB | Display | ![]() |
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Full document | ![]() | 829 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 48.1 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21204.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 24399.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Fusion protein consists of moth cytochrome C peptide, residues 1-14 (ADLIAYLKQATK), Glycine rich linker, residues 15-30 (GGGGSLVPRGSGGGGS) and mouse MHC E-beta-k chain Source: (gene. exp.) Lonomia obliqua, Mus musculus / Genus: Lonomia, Mus / Species: , / Strain: , / Cell line (production host): SF9 / Production host: ![]() ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.96 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG4000, 2-propanol, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: STORAGE PHOSPHORS / Date: Jan 1, 1996 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 26119 / Num. obs: 22827 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.1 Å2 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible all: 93.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS % possible obs: 93.4 % / Num. unique obs: 3185 / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.0734 Å2 / ksol: 0.305321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.221 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.89 Å / Rfactor Rfree: 0.422 / Num. reflection Rfree: 85 / Rfactor Rwork: 0.322 / Num. reflection Rwork: 1845 / Rfactor obs: 0.322 |