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Yorodumi- PDB-1mhe: THE HUMAN NON-CLASSICAL MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mhe | ||||||
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Title | THE HUMAN NON-CLASSICAL MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE HLA-E | ||||||
Components |
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Keywords | MAJOR HISTOCOMPATIBILITY COMPLEX / HLA-E / HLA E / MHC / HLA / BETA 2 MICROGLOBULIN / LEADER PEPTIDE / NON-CLASSICAL MHC / CLASS IB MHC | ||||||
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 / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / 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 / 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 / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / 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 / ER to Golgi transport vesicle membrane / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | O'Callaghan, C.A. / Tormo, J. / Willcox, B.E. / Braud, V.B. / Jakobsen, B.K. / Stuart, D.I. / Mcmichael, A.J. / Bell, J.I. / Jones, E.Y. | ||||||
Citation | Journal: Mol.Cell / Year: 1998 Title: Structural features impose tight peptide binding specificity in the nonclassical MHC molecule HLA-E. Authors: O'Callaghan, C.A. / Tormo, J. / Willcox, B.E. / Braud, V.M. / Jakobsen, B.K. / Stuart, D.I. / McMichael, A.J. / Bell, J.I. / Jones, E.Y. #1: Journal: Protein Sci. / Year: 1998 Title: Production, Crystallization, and Preliminary X-Ray Analysis of the Human Mhc Class Ib Molecule Hla-E Authors: O'Callaghan, C.A. / Tormo, J. / Willcox, B.E. / Blundell, C.D. / Jakobsen, B.K. / Stuart, D.I. / Mcmichael, A.J. / Bell, J.I. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mhe.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mhe.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/1mhe ftp://data.pdbj.org/pub/pdb/validation_reports/mh/1mhe | HTTPS FTP |
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-Related structure data
Related structure data | 3hlaS 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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Unit cell |
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-Components
#1: Protein | Mass: 31697.854 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, ALPHA CHAIN E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: DENATURED AND REFOLDED IN THE PRESENCE OF PEPTIDE AND BETA-2-MICROGLOBULIN Cell line: BL21 / Gene: HLA-E / Plasmid: COC057 / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / 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) / Cell line: BL21 / Gene: BETA-2-MICROGLOBULIN / Plasmid: PHN1 / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): XA 90 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1000.278 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SYNTHESISED CHEMICALLY #4: Chemical | ChemComp-SO4 / | #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: 4.75 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.04 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRROR 1 AND MIRROR 2 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→25 Å / Num. obs: 37611 / % possible obs: 95.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 70.12 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.25 |
Reflection shell | Resolution: 2.85→3.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.1 / % possible all: 85.7 |
Reflection | *PLUS Num. measured all: 248512 |
Reflection shell | *PLUS % possible obs: 85.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HLA Resolution: 2.85→25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: IT SHOULD BE NOTED THAT THE APPLICATION OF OVERALL ANISOTROPIC B SCALING LED TO A SIGNIFICANT INCREASE OF THE TEMPERATURE FACTORS.
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Displacement parameters | Biso mean: 51.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.85→3.1 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.32 |