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Yorodumi- PDB-1p7q: Crystal Structure of HLA-A2 Bound to LIR-1, a Host and Viral MHC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p7q | ||||||
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Title | Crystal Structure of HLA-A2 Bound to LIR-1, a Host and Viral MHC Receptor | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA-A2-Lir-1 Complex | ||||||
Function / homology | Function and homology information HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / negative regulation of serotonin secretion / dendritic cell differentiation / protein phosphatase 1 binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of interferon-beta production / negative regulation of endocytosis / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / T cell proliferation involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-10 production / negative regulation of calcium ion transport / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of type II interferon production / positive regulation of memory T cell activation / TAP complex binding / negative regulation of tumor necrosis factor production / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / negative regulation of cell cycle / 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 / MHC class I protein binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / positive regulation of defense response to virus by host / 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 / detection of bacterium / SH2 domain binding / 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 / response to virus / HIV-1 retropepsin / 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 / retroviral ribonuclease H / exoribonuclease H / 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 / : / exoribonuclease H activity / receptor internalization / 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 / host multivesicular body / 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 / DNA integration / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cytokine-mediated signaling pathway / cellular response to nicotine / RNA-directed DNA polymerase Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Willcox, B.E. / Thomas, L.M. / Bjorkman, P.J. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2003 Title: Crystal structure of HLA-A2 bound to LIR-1, a host and viral major histocompatibility complex receptor. Authors: Willcox, B.E. / Thomas, L.M. / Bjorkman, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p7q.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p7q.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/1p7q ftp://data.pdbj.org/pub/pdb/validation_reports/p7/1p7q | HTTPS FTP |
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-Related 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: 31951.316 Da / Num. of mol.: 1 / Fragment: residue 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A OR HLAA / Plasmid: BJ075 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS (DE3) / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: BJ192 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS (DE3) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 993.199 Da / Num. of mol.: 1 / Fragment: residue 463-471 / Source method: obtained synthetically / References: UniProt: P12499 |
#4: Protein | Mass: 21998.645 Da / Num. of mol.: 1 / Fragment: residue 25-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS (DE3) / References: UniProt: Q8NHL6 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.27 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Sodium Acetate, Tris, L-Cysteine, Triton X-100, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.992 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2001 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 9493 / Num. obs: 9493 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.4→3.61 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.8 / Num. unique all: 928 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 61195 / Rmerge(I) obs: 0.18 |
Reflection shell | *PLUS Lowest resolution: 3.5 Å / % possible obs: 100 % / Num. unique obs: 928 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1G0X and 1AKJ Resolution: 3.4→33.11 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 2117689.07 / Data cutoff high rms absF: 2117689.07 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.846 Å2 / ksol: 0.298764 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→33.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.222 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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