+Open data
-Basic information
Entry | Database: PDB / ID: 8d5n | ||||||
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Title | Crystal structure of Ld-HF10 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHCI / antigen / CD8 T cell | ||||||
Function / homology | Function and homology information 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 tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...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 tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / 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 / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / 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 / MHC class I protein binding / cellular defense response / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / lumenal side of endoplasmic reticulum membrane / 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 / defense response / peptide antigen assembly with MHC class I protein complex / 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 / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / protein-folding chaperone binding / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wang, Y. / Dai, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Immunol / Year: 2022 Title: Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response. Authors: Wang, Y. / Tsitsiklis, A. / Devoe, S. / Gao, W. / Chu, H.H. / Zhang, Y. / Li, W. / Wong, W.K. / Deane, C.M. / Neau, D. / Slansky, J.E. / Thomas, P.G. / Robey, E.A. / Dai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d5n.cif.gz | 304.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d5n.ent.gz | 238.8 KB | Display | PDB format |
PDBx/mmJSON format | 8d5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5n ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5n | HTTPS FTP |
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-Related structure data
Related structure data | 8d5pC 8d5qC 1ld9S 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules CAFH
#1: Protein | Mass: 32402.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01897 #3: Protein | Mass: 11975.634 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887 |
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-Protein/peptide / Sugars , 2 types, 4 molecules EB
#2: Protein/peptide | Mass: 1567.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: GRA6, TG24 / Production host: Podospora comata (fungus) #4: Sugar | |
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-Non-polymers , 4 types, 405 molecules
#5: Chemical | ChemComp-PG4 / | ||
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#6: Chemical | ChemComp-PPI / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3.05 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH5.5, and 1M Lithium sulfate monohydrate |
-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: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→77 Å / Num. obs: 102152 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.23 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.738 / Num. unique obs: 17831 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LD9 Resolution: 1.8→50.005 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.178 / SU B: 5.793 / SU ML: 0.084 / Average fsc free: 0.8911 / Average fsc work: 0.9049 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.107 Details: Hydrogens have been added in their riding positions
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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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.482 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50.005 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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