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Yorodumi- PDB-3quk: Crystal structures of the murine class I major histocompatibility... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3quk | ||||||
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Title | Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 altered peptide ligand (Y4A) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Murine MHC / LCMV / receptor binding / beta2-microglobulin / T cell recognition / T cell receptor / cell surface | ||||||
Function / homology | Function and homology information 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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / host cell Golgi membrane / 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 / peptide binding / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / 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 / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Lymphocytic choriomeningitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Allerbring, E. / Duru, A.D. / Uchtenhagen, H. / Madhurantakam, C. / Grimm, S. / Tomek, M.B. / Mazumdar, P.A. / Spetz, A. / Friemann, R. / Sandalova, T. ...Allerbring, E. / Duru, A.D. / Uchtenhagen, H. / Madhurantakam, C. / Grimm, S. / Tomek, M.B. / Mazumdar, P.A. / Spetz, A. / Friemann, R. / Sandalova, T. / Uhlin, M. / Nygren, P. / Achour, A. | ||||||
Citation | Journal: Eur.J.Immunol. / Year: 2012 Title: Unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics. Authors: Allerbring, E.B. / Duru, A.D. / Uchtenhagen, H. / Madhurantakam, C. / Tomek, M.B. / Grimm, S. / Mazumdar, P.A. / Friemann, R. / Uhlin, M. / Sandalova, T. / Nygren, P.A. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3quk.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3quk.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 3quk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3quk_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 3quk_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 3quk_validation.xml.gz | 31 KB | Display | |
Data in CIF | 3quk_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/3quk ftp://data.pdbj.org/pub/pdb/validation_reports/qu/3quk | HTTPS FTP |
-Related structure data
Related structure data | 3qulC 1s7uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 2 / Auth seq-ID: 1 - 99 / Label seq-ID: 1 - 99
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-Components
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 2 / Fragment: UNP Residues 25-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: Pet3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: UNP Residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: Pet3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 #3: Protein/peptide | Mass: 953.135 Da / Num. of mol.: 2 / Fragment: UNP Residues 33-41 / Mutation: Y4A & C9M / Source method: obtained synthetically / Details: This sequence occurs naturally in LCMV / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399 #4: 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: 3.32 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.8 M ammonium sulfate, 0.1 M Tris HCl pH 9.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.007 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→36.2 Å / Num. all: 44615 / Num. obs: 44615 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.7 / Num. unique all: 5419 / Rsym value: 0.213 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S7U Resolution: 2.41→33.9 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.878 / SU B: 8.221 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.275 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→33.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.41→2.473 Å / Total num. of bins used: 20
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