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Yorodumi- PDB-1ktl: The human non-classical major histocompatibility complex molecule... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ktl | ||||||
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Title | The human non-classical major histocompatibility complex molecule HLA-E | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA-E / MHC / NON-CLASSICAL MHC / HLA / BETA 2 MICROGLOBULIN | ||||||
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 ...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 / : / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of interleukin-13 production / retina homeostasis / 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 CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor 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 ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / RIGID-BODY REFINEMENT OF 1KPR / Resolution: 3.1 Å | ||||||
Authors | Holmes, M.A. / Strong, R.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: HLA-E allelic variants: Correlating differential expression, peptide affinities, crystal structures and thermal stabilities Authors: Strong, R.K. / Holmes, M.A. / Li, P. / Braun-Jones, L. / Lee, N. / Geraghty, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ktl.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ktl.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ktl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ktl_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 1ktl_full_validation.pdf.gz | 459 KB | Display | |
Data in XML | 1ktl_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 1ktl_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1ktl ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1ktl | HTTPS FTP |
-Related structure data
Related structure data | 1kprSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 31511.596 Da / Num. of mol.: 2 / Mutation: R107G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E / Production host: Escherichia coli (E. coli) / Strain (production host): UBS / References: UniProt: P13747 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P01884, UniProt: P61769*PLUS #3: Protein/peptide | Mass: 984.213 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-SO4 / | |
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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: 4.52 Å3/Da / Density % sol: 72.78 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, PEG 400, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K, pH 8.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||
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 IV / Detector: IMAGE PLATE / Date: Jul 12, 1999 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→25 Å / Num. all: 27568 / Num. obs: 27568 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 85.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 3.1→3.15 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1230 / % possible all: 84.1 |
Reflection | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 25 Å / Num. measured all: 265243 |
Reflection shell | *PLUS Highest resolution: 3.1 Å / % possible obs: 84.1 % |
-Processing
Software |
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Refinement | Method to determine structure: RIGID-BODY REFINEMENT OF 1KPR Starting model: PDB ENTRY 1KPR Resolution: 3.1→25 Å / Isotropic thermal model: ISOTROPIC GROUP B'S / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 63 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.28 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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