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Open data
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Basic information
Entry | Database: PDB / ID: 1nan | ||||||
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Title | MCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE | ||||||
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![]() | IMMUNE SYSTEM / class I MHC / H-2Kb / alloreactivity / crossreactivity | ||||||
Function / homology | ![]() Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / positive regulation of phosphorylation / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B. | ||||||
![]() | ![]() Title: CDR3 loop flexibility contributes to the degeneracy of TCR recognition Authors: Reiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B. #1: ![]() Title: A T-Cell Receptor Cdr3Beta Loop Undergoes Conformational Changes of Unprecedented Magnitude Upon Binding to a Peptide/Mhc Class I Complex Authors: Reiser, J.-B. / Gregoire, C. / Darnault, C. / Mosser, T. / Guimezanes, A. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Mazza, G. / Malissen, B. / Housset, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 132.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.4 KB | Display | ![]() |
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Full document | ![]() | 489.2 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1namC ![]() 1kj3S 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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Unit cell |
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Components
#1: Protein | Mass: 32068.777 Da / Num. of mol.: 2 / Fragment: Extracellular Domains (alpha1, alpha2, alpha3) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 983.076 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence is naturally found in mus muculus (mouse). References: GenBank: 13385376, UniProt: Q8CDD8*PLUS #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.73 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG6000 16-17%, NaAc 0.2M, NaCl 0.3M, Mes 0.1M, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.26 Å / Num. all: 41983 / Num. obs: 41983 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.067 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 5761 / Rsym value: 0.272 / % possible all: 97.3 |
Reflection | *PLUS Lowest resolution: 61.3 Å / % possible obs: 98.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.27 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KJ3 Resolution: 2.3→12 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å
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Refinement | *PLUS Rfactor Rfree: 0.278 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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