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Yorodumi- PDB-2ve6: Crystal structure of a Murine MHC class I H2-Db molecule in compl... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2ve6 | |||||||||
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| Title | Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / PHOTOCLEAVABLE PEPTIDE / AUXILIARY ANCHORING RESIDUE / GLYCOPROTEIN / TRANSMEMBRANE / PEPTIDE LOADING / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / MHC / SEV9 / MHC I / MEMBRANE / SECRETED | |||||||||
| Function / homology | Function and homology informationEndosomal/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 / regulation of membrane depolarization / antigen processing and presentation of peptide antigen via MHC class I / 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 / regulation of membrane depolarization / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein refolding / cellular response to lipopolysaccharide / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / immune response / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() SENDAI VIRUS | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Grotenbreg, G.M. / Roan, N.R. / Guillen, E. / Meijers, R. / Wang, J.H. / Bell, G.W. / Starnbach, M.N. / Ploegh, H.L. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008Title: Discovery of Cd8+ T Cell Epitopes in Chlamydia Trachomatis Infection Through Use of Caged Class I Mhc Tetramers. Authors: Grotenbreg, G.M. / Roan, N.R. / Guillen, E. / Meijers, R. / Wang, J.H. / Bell, G.W. / Starnbach, M.N. / Ploegh, H.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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2ve6.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2ve6.ent.gz | 258.7 KB | Display | PDB format |
| PDBx/mmJSON format | 2ve6.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2ve6 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2ve6 | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 1wbxS S: Starting model for refinement |
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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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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
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Components
| #1: Protein | Mass: 32184.816 Da / Num. of mol.: 4 / Fragment: RESIDUES 25-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 11678.388 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein/peptide | Mass: 1044.117 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 3-AMINO-3-(2-NITRO)PHENYL-PROPIONIC ACID AT P7 / Source: (synth.) SENDAI VIRUS#4: Water | ChemComp-HOH / | Has protein modification | Y | Nonpolymer details | 3-AMINO-3-(2-NITRO)PHENYL-PROPIONIC ACID (PRQ): PHOTOCLEAV | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION |
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Sample preparation
| Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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| Crystal grow | Method: vapor diffusion, hanging drop Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE AND 0.1 M CACODYLATE AT PH 6.4. |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07 |
| Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 25, 2005 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
| Reflection | Resolution: 2.65→20 Å / Num. obs: 50561 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1WBX Resolution: 2.65→19.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.873 / SU B: 34.083 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / 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: 47.84 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.65→19.66 Å
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| Refine LS restraints |
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SENDAI VIRUS
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