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Yorodumi- PDB-1fzm: MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BET... -
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-Basic information
Entry | Database: PDB / ID: 1fzm | |||||||||
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Title | MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / major histocompatibility complex peptide-MHC | |||||||||
Function / homology | Function and homology information TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / helical viral capsid / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / positive regulation of natural killer cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of immunoglobulin production / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / iron ion transport / antibacterial humoral response / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / cellular response to lipopolysaccharide / host cell cytoplasm / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / early endosome / defense response to Gram-positive bacterium / defense response to bacterium / immune response Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / CNS, done by rigid body refinement of starting model. / Resolution: 1.8 Å | |||||||||
Authors | Rudolph, M.G. / Speir, J.A. / Brunmark, A. / Mattsson, N. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | |||||||||
Citation | Journal: Immunity / Year: 2001 Title: The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity. Authors: Rudolph, M.G. / Speir, J.A. / Brunmark, A. / Mattsson, N. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fzm.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fzm.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzm ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzm | HTTPS FTP |
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-Related structure data
Related structure data | 1fzjC 1fzkC 1fzoC 2vaaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31587.264 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN / Mutation: Y22F, M23I, E24S, D30N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901 |
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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.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887 |
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 956.078 Da / Num. of mol.: 1 / Fragment: RESIDUES 52-59 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is found naturally in Vesicular stomatitis virus. References: UniProt: P11212 |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 281 molecules
#6: Chemical | #7: Chemical | ChemComp-MRD / ( | #8: Chemical | #9: 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 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: K/Na phosphate, MPD , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.1 Å / Num. all: 49672 / Num. obs: 49672 / % possible obs: 95.1 % / Observed criterion σ(I): 2.5 / Redundancy: 2.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.8→1.82 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1565 / % possible all: 91.9 |
Reflection shell | *PLUS % possible obs: 91.9 % / Num. unique obs: 1565 |
-Processing
Software |
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Refinement | Method to determine structure: CNS, done by rigid body refinement of starting model. Starting model: pdb-entry 2vaa without peptide, water, and mutated side chains truncated to alanine. Resolution: 1.8→22.07 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 56662868.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.58 Å2 / ksol: 0.391 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→22.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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