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- PDB-1kj2: Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kj2 | |||||||||
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Title | Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex | |||||||||
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![]() | IMMUNE SYSTEM / T CELL RECEPTOR / CLASS I MHC / H-2KB / TCR-PMHC COMPLEX / ALLOGENEIC | |||||||||
Function / homology | ![]() alpha-aminoacyl-tRNA binding / cytoplasmic exosome (RNase complex) / positive regulation of mRNA catabolic process / GTP metabolic process / 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 ...alpha-aminoacyl-tRNA binding / cytoplasmic exosome (RNase complex) / positive regulation of mRNA catabolic process / GTP metabolic process / 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 / T cell receptor complex / translational elongation / 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 / translation elongation factor activity / 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 / adaptive immune response / amyloid fibril formation / tRNA binding / cytoplasmic translation / learning or memory / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / GTPase activity / protein-containing complex binding / GTP binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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. #1: ![]() Title: The three-dimentional structure of a T-cell antigen receptor ValphaVbeta heterodimer reveals a novel arrangement of the Vbeta domain Authors: Housset, D. / Mazza, G. / Gregoire, C. / Piras, C. / Malissen, B. / Fontecilla-Camps, J.C. #2: ![]() Title: CRYSTAL STRUCTURE OF A T CELL RECEPTOR BOUND TO AN ALLOGENIC MHC MOLECULE Authors: Reiser, J.-B. / Darnault, C. / Guimezanes, A. / Gregoire, C. / Mosser, T. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Malissen, B. / Housset, D. / Mazza, G. #3: ![]() Title: IDENTIFICATION OF ENDOGENEOUS PEPTIDES RECOGNIZED BU IN VIVO OR IN VITRO GENERATED ALLOREACTIVE CTL: DISTINCT CHARACTERISTICS CORRELATED WITH CD8-DEPENDENCE Authors: Guimezanes, A. / Barret-Wilt, G. / Gulden-Thompson, P. / Shabanowitz, J. / Hunt, D. / Schmitt-Verhulst, A.-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 | ![]() | 263.5 KB | Display | ![]() |
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PDB format | ![]() | 211 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 912.9 KB | Display | ![]() |
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Full document | ![]() | 965.7 KB | Display | |
Data in XML | ![]() | 51.4 KB | Display | |
Data in CIF | ![]() | 70.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kj3SC ![]() 1kb5S 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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules HILM
#1: Protein | Mass: 31971.664 Da / Num. of mol.: 2 / Fragment: Extracellular domains (alpha1, alpha2, alpha3) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 11704.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-KB5-C20 T-Cell receptor ... , 2 types, 4 molecules ADBE
#4: Protein | Mass: 12478.844 Da / Num. of mol.: 2 / Fragment: Fv fragment , variable domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #5: Protein | Mass: 13381.247 Da / Num. of mol.: 2 / Fragment: Fv fragment , variable domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide / Non-polymers , 2 types, 93 molecules PQ![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#2: Protein/peptide | Mass: 949.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURS IN MUS MUCULUS / References: UniProt: O08582 #8: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#6: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 17-19% PEG 6000, 0.1M Mes, 0.1M NaCl, 0.1M MgAc, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→14.99 Å / Num. all: 45992 / Num. obs: 45992 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 55.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.71→2.85 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 4916 / Rsym value: 0.382 / % possible all: 87.8 |
Reflection | *PLUS Highest resolution: 2.7 Å / Rmerge(I) obs: 0.084 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KB5, 1KJ3 Resolution: 2.71→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The work R and Free R values correspond to the ones calulated in the last cycle of maximum likelihood refinement. Due to the resolution limit of our structure (2.7), The refinement has been ...Details: The work R and Free R values correspond to the ones calulated in the last cycle of maximum likelihood refinement. Due to the resolution limit of our structure (2.7), The refinement has been ended by few cycles of least-square method including all reflexions. So both distinct algorithms and the including of Free set in refinement can make the convergence a little different.
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Solvent computation | Bsol: 26.56 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.81 Å
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.362 |