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Yorodumi- PDB-1ffn: CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ffn | ||||||
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Title | CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE GP33(C9M) | ||||||
Components |
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Keywords | IMMUNE SYSTEM/SIGNALING PROTEIN / major histocompatibility complex / peptide binding / T cell receptor / IMMUNE SYSTEM-SIGNALING PROTEIN COMPLEX | ||||||
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 / 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 / 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 / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Wang, B. / Sharma, A. / Maile, R. / Saad, M. / Collins, E.J. / Frelinger, J.A. | ||||||
Citation | Journal: J.IMMUNOL. / Year: 2002 Title: Peptidic termini play a significant role in TCR recognition Authors: Wang, B. / Sharma, A. / Maile, R. / Saad, M. / Collins, E.J. / Frelinger, J.A. #1: Journal: J.EXP.MED. / Year: 1999 Title: Structural evidence of T cell xeno reactivity in the absence of molecular mimicry Authors: Zhao, R. / Loftus, D.J. / Apella, E. / Collins, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ffn.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ffn.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ffn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ffn_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 1ffn_full_validation.pdf.gz | 497.2 KB | Display | |
Data in XML | 1ffn_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 1ffn_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ffn ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ffn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | H-2 Db heavy chain is noncovalently associted to beta-2 microglobulin light chain. Heavy chain comprises of three subunits alpha1, alpha2 and alpha3. Peptide binds in the groove formed by the alpha1 and alpha2 domains of heavy chain. |
-Components
#1: Protein | Mass: 31804.420 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR PORTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899 #2: Protein | Mass: 11835.555 Da / Num. of mol.: 2 / Fragment: BETA-2 MICROGLOBULIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 #3: Protein/peptide | Mass: 1045.232 Da / Num. of mol.: 2 / Fragment: GP33 PEPTIDE WITH SUBSTITUTION / Mutation: C9M / Source method: obtained synthetically / Details: The peptide was synthesized. #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: 2.61 Å3/Da / Density % sol: 52.96 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14% PEG8000, 1% Dioxane, 25mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 22352 / Num. obs: 22352 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 2 % / Rmerge(I) obs: 0.354 / Num. unique all: 3591 / % possible all: 85.6 |
Reflection | *PLUS Num. measured all: 99827 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / % possible obs: 85.6 % / Mean I/σ(I) obs: 1.98 |
-Processing
Software |
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Refinement | Resolution: 2.7→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 721708.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum Likelihood function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.52 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.43 |