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Yorodumi- PDB-6ewo: Crystal structure of non-phosphorylated form of RTF PHOSPHOPEPTID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ewo | ||||||
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Title | Crystal structure of non-phosphorylated form of RTF PHOSPHOPEPTIDE BOUND TO HLA-A2 in complex with LILRB1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / LILRB1 / NONPHOSPHOPEPTIDE / peptide-MHC complex / HLA-A2 / tumour antigen / crystallisation chaperone | ||||||
Function / homology | Function and homology information fast-twitch skeletal muscle fiber contraction / neurofilament cytoskeleton / intermediate filament binding / 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 ...fast-twitch skeletal muscle fiber contraction / neurofilament cytoskeleton / intermediate filament binding / 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 / intermediate filament cytoskeleton organization / dendritic cell differentiation / vinculin binding / 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 / costamere / 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 / intermediate filament / T cell proliferation involved in immune response / structural constituent of muscle / intermediate filament cytoskeleton / 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 / adherens junction / sarcolemma / response to virus / 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 / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / structural constituent of cytoskeleton / 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 / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Model details | ================CATEGORY 5: Authors of Structure============================ Enter authors of the ...================CATEGORY 5: Authors of Structure============================ Enter authors of the deposited structures (e.g. Surname, F.M.) | ||||||
Authors | Mohammed, F. / Stones, D.H. / Willcox, B.E. | ||||||
Citation | Journal: J. Immunol. Methods / Year: 2019 Title: Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes. Authors: Mohammed, F. / Stones, D.H. / Willcox, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ewo.cif.gz | 240.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ewo.ent.gz | 192.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ewo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/6ewo ftp://data.pdbj.org/pub/pdb/validation_reports/ew/6ewo | HTTPS FTP |
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-Related structure data
Related structure data | 6ewaC 6ewcC 1p7qS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P61769 #3: Protein/peptide | Mass: 1042.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMMERCIAL SYNTHESIS / Source: (synth.) Homo sapiens (human) / References: UniProt: O15061 #4: Protein | Mass: 21747.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: D9IDM8, UniProt: Q8NHL6*PLUS #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: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 25, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→19.7 Å / Num. obs: 66969 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.331 % / Biso Wilson estimate: 38.572 Å2 / Rmerge F obs: 0.113 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.105 / Χ2: 0.876 / Net I/σ(I): 23.61 / Num. measured all: 758810 / Scaling rejects: 103 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P7Q Resolution: 2.3→19.7 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.051 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.249 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.52 Å2 / Biso mean: 37.859 Å2 / Biso min: 12.79 Å2
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Refinement step | Cycle: final / Resolution: 2.3→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.362 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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