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Yorodumi- PDB-1kt2: CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTO... -
+Open data
-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 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Protein-peptide complex / T cell receptor / antigen presentation / cytochrome | |||||||||
Function / homology | Function and homology information 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 / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...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 / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / 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 / MHC class II antigen presentation / positive regulation of memory T cell differentiation / CD4 receptor binding / polysaccharide binding / immunoglobulin mediated immune response / immunological synapse / T cell receptor binding / cognition / positive regulation of T cell mediated cytotoxicity / 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 / cell surface / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Lonomia obliqua (butterflies/moths) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Fremont, D.H. / Dai, S. / Chiang, H. / Crawford, F. / Marrack, P. / Kappler, J. | |||||||||
Citation | Journal: J.Exp.Med. / Year: 2002 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kt2.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kt2.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kt2 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kt2 | HTTPS FTP |
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-Related structure data
-Links
-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.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01904 #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: Spodoptera frugiperda (fall armyworm) / References: GenBank: 199396, UniProt: P04230*PLUS #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.93 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 254361.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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 |