+Open data
-Basic information
Entry | Database: PDB / ID: 3kyo | ||||||
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Title | Crystal structure of HLA-G presenting KLPAQFYIL peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human leukocyte antigen / major histocompatibility complex / immune response / MHC I | ||||||
Function / homology | Function and homology information peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of T cell mediated cytotoxicity / positive regulation of natural killer cell cytokine production / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of G0 to G1 transition ...peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of T cell mediated cytotoxicity / positive regulation of natural killer cell cytokine production / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of regulatory T cell differentiation / positive regulation of endothelial cell apoptotic process / filopodium membrane / positive regulation of macrophage cytokine production / CD8 receptor binding / protein homotrimerization / protection from natural killer cell mediated cytotoxicity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular defense response / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / negative regulation of angiogenesis / 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 / 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 / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / 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 / recycling endosome membrane / specific granule lumen / 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 / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / early endosome / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Walpole, N.G. / Rossjohn, J. / Clements, C.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: The structure and stability of the monomorphic HLA-G are influenced by the nature of the bound peptide Authors: Walpole, N.G. / Kjer-Nielsen, L. / Kostenko, L. / McCluskey, J. / Brooks, A.G. / Rossjohn, J. / Clements, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kyo.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kyo.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/3kyo ftp://data.pdbj.org/pub/pdb/validation_reports/ky/3kyo | HTTPS FTP |
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-Related structure data
Related structure data | 3kynC 1ydpS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31601.002 Da / Num. of mol.: 2 / Fragment: residues in UNP 26-298 / Mutation: C66S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-G / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: Q9MYA2, UniProt: P17693*PLUS #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, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1093.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesised peptide #4: Chemical | #5: 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: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 16% PEG 3350, 0.2M potassium formate, 0.1M HEPES, 10mM cobalt chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→43 Å / Num. obs: 119833 / Rmerge(I) obs: 0.082 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YDP Resolution: 1.7→43 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.798 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.139 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.702→1.746 Å / 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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