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Yorodumi- PDB-8fhl: Structure of pyruvate dehydrogenase phosphatase regulatory subuni... -
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-Basic information
Entry | Database: PDB / ID: 8fhl | ||||||
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Title | Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / neoepitope / Mouse / Pdpr | ||||||
Function / homology | Function and homology information pyruvate dehydrogenase (lipoamide) phosphatase complex / positive regulation of pyruvate dehydrogenase activity / Regulation of pyruvate dehydrogenase (PDH) complex / 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 ...pyruvate dehydrogenase (lipoamide) phosphatase complex / positive regulation of pyruvate dehydrogenase activity / Regulation of pyruvate dehydrogenase (PDH) complex / 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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding / Neutrophil degranulation / protein dephosphorylation / 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 / peptide binding / 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 / response to molecule of bacterial origin / 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 / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / oxidoreductase activity / learning or memory / mitochondrial matrix / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å | ||||||
Authors | Custodio, J.M.F. / Baker, B.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of Pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd Authors: Custodio, J.M.F. / Baker, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fhl.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fhl.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fhl ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fhl | HTTPS FTP |
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-Related structure data
Related structure data | 8fhuC 8d5fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32265.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01900 |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 954.145 Da / Num. of mol.: 1 / Fragment: neoepitope (UNP residues 627-635) / Mutation: V632L / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8NCN5 |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium isothiocyanate, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.343 Å / Num. obs: 29908 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.055 / Rrim(I) all: 0.195 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 2215 / CC1/2: 0.367 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8D5F Resolution: 2.194→41.343 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.236 / SU ML: 0.167 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.203 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.643 Å2
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Refinement step | Cycle: LAST / Resolution: 2.194→41.343 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection: ALL |