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- PDB-3bze: The human non-classical major histocompatibility complex molecule... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bze | ||||||
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Title | The human non-classical major histocompatibility complex molecule HLA-E | ||||||
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![]() | IMMUNE SYSTEM / MHC fold / Transmembrane / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted | ||||||
Function / homology | ![]() peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / 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 ...peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / 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 T cell mediated cytotoxicity / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of endothelial cell apoptotic process / positive regulation of regulatory T cell differentiation / filopodium membrane / positive regulation of natural killer cell proliferation / positive regulation of macrophage cytokine production / 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 / CD8 receptor binding / positive regulation of interleukin-4 production / MHC class I protein binding / protein homotrimerization / protection from natural killer cell mediated cytotoxicity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / negative regulation of angiogenesis / 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 / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoare, H.L. / Sullivan, L.C. / Ely, L.K. / Beddoe, T. / Henderson, K.N. / Lin, J. / Clements, C.S. / Reid, H.H. / Brooks, A.G. / Rossjohn, J. | ||||||
![]() | ![]() Title: Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors Authors: Hoare, H.L. / Sullivan, L.C. / Clements, C.S. / Ely, L.K. / Beddoe, T. / Henderson, K.N. / Lin, J. / Reid, H.H. / Brooks, A.G. / Rossjohn, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.8 KB | Display | ![]() |
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PDB format | ![]() | 260.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 523.7 KB | Display | ![]() |
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Full document | ![]() | 612.3 KB | Display | |
Data in XML | ![]() | 67.2 KB | Display | |
Data in CIF | ![]() | 90.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bzfC ![]() 1mheS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31640.803 Da / Num. of mol.: 4 / Fragment: residues 2-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1048.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P17693 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 14-19% PEG 3350, 2% MPD, 0.2M MgCl2, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 63040 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.6 |
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Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 1MHE Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.882 / SU B: 29.343 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.048 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.501→2.565 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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