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- PDB-1wby: CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES ... -
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Basic information
Entry | Database: PDB / ID: 1wby | ||||||
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Title | CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE | ||||||
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![]() | IMMUNE SYSTEM / MHC CLASS I / INFLUENZA PEPTIDE / PA224 / IMMMUNE SYSTEM | ||||||
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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation ...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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / 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 / immune response / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meijers, R. / Lai, C. / Yang, Y. / Liu, J. / Zhong, W. / Wang, J. / Reinherz, E.L. | ||||||
![]() | ![]() Title: Crystal Structures of Murine Mhc Class I H-2 D(B) and K(B) Molecules in Complex with Ctl Epitopes from Influenza a Virus: Implications for Tcr Repertoire Selection and Immunodominance Authors: Meijers, R. / Lai, C. / Yang, Y. / Liu, J. / Zhong, W. / Wang, J. / Reinherz, E.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 97 KB | Display | ![]() |
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PDB format | ![]() | 74.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.4 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wbxC ![]() 1wbzC ![]() 1jpfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1186.295 Da / Num. of mol.: 1 / Fragment: RESIDUES 224-233 / Source method: obtained synthetically / Details: PEPTIDE DERIVED FROM PR8 INFLUENZA A PA224-233 / Source: (synth.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.16 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 19939 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 2.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JPF Resolution: 2.3→29.58 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.867 / SU B: 8.278 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.58 Å
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