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Yorodumi- PDB-3fon: Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Sing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fon | |||||||||
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Title | Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFEAI | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Class I MHC / peptide complex / Diabetes-protective Effect / Immune response / Immunoglobulin domain / MHC I / Secreted | |||||||||
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 / 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 ...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 / 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 / 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 / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å | |||||||||
Authors | Malashkevich, V.N. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. ...Malashkevich, V.N. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Ramagopal, U.A. / Brims, D.R. / Almo, S.C. / Nathenson, S.G. / DiLorenzo, T.P. | |||||||||
Citation | Journal: Int.Immunol. / Year: 2010 Title: Predominant occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its diabetes-protective effect. Authors: Brims, D.R. / Qian, J. / Jarchum, I. / Mikesh, L. / Palmieri, E. / Ramagopal, U.A. / Malashkevich, V.N. / Chaparro, R.J. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Nathenson, ...Authors: Brims, D.R. / Qian, J. / Jarchum, I. / Mikesh, L. / Palmieri, E. / Ramagopal, U.A. / Malashkevich, V.N. / Chaparro, R.J. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Nathenson, S.G. / Almo, S.C. / Dilorenzo, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fon.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fon.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 3fon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fon_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 3fon_full_validation.pdf.gz | 474.8 KB | Display | |
Data in XML | 3fon_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 3fon_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/3fon ftp://data.pdbj.org/pub/pdb/validation_reports/fo/3fon | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999
NCS ensembles :
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-Components
#1: Protein | Mass: 31487.088 Da / Num. of mol.: 2 / Fragment: MHC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / References: UniProt: D2YW38*PLUS #2: Protein | Mass: 11835.555 Da / Num. of mol.: 2 / Fragment: IgC 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) / References: UniProt: P01887 #3: Protein/peptide | Mass: 920.018 Da / Num. of mol.: 2 / Fragment: Peptide / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) synthetic construct (others) #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: 2.88 Å3/Da / Density % sol: 57.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3000, 100 mM HEPES, pH 7.5, 200 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.03→50 Å / Num. obs: 64629 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.136 / Net I/σ(I): 18.964 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.734 / SU B: 9.23 / SU ML: 0.12 / SU R Cruickshank DPI: 0.197 / SU Rfree: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 93.68 Å2 / Biso mean: 27.276 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.032→2.084 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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