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- PDB-4no0: Crystal structure of non-phosphorylated form of RQA_V phosphopept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4no0 | ||||||
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Title | Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1 | ||||||
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![]() | IMMUNE SYSTEM/ANTIGEN / Nonphosphorylated peptide / peptide-MHC complex / MHC / LILRB1 / post translational modification / peptide conformation / tumor immunology / tumor antigen / neoepitope / IMMUNE SYSTEM-ANTIGEN complex | ||||||
Function / homology | ![]() 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 / HLA-B specific inhibitory MHC class I receptor activity / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity ...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 / HLA-B specific inhibitory MHC class I receptor activity / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity / immune response-regulating signaling pathway / 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 serotonin secretion / negative regulation of cytokine production involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / dendritic cell differentiation / interleukin-10-mediated signaling pathway / negative regulation of mononuclear cell proliferation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / cellular response to interleukin-7 / positive regulation of macrophage cytokine production / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / CD8 receptor binding / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / negative regulation of calcium ion transport / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / TAP binding / negative regulation of cell cycle / protection from natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / positive regulation of defense response to virus by host / SH2 domain binding / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / response to virus / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / receptor internalization / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mohammed, F. / Stones, D.H. / Willcox, B.E. | ||||||
![]() | ![]() Title: The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status. Authors: Mohammed, F. / Stones, D.H. / Zarling, A.L. / Willcox, C.R. / Shabanowitz, J. / Cummings, K.L. / Hunt, D.F. / Cobbold, M. / Engelhard, V.H. / Willcox, B.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.7 KB | Display | ![]() |
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PDB format | ![]() | 102.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nnxC ![]() 4nnyC ![]() 4no2C ![]() 4no3C ![]() 4no5C ![]() 1p7qS 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
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 25-300) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 21747.340 Da / Num. of mol.: 1 / Fragment: UNP residues 27-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1302.520 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 249-260) / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 2 types, 49 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EDO / |
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#6: Water | ChemComp-HOH / |
-Details
Sequence details | IN LEUKOCYTE IMMUNOGLOB |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG3350, 0.1 M HEPES, pH 7.4, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 21, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→29.325 Å / Num. obs: 21132 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 36 % / Biso Wilson estimate: 47.502 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 33.28 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P7Q Resolution: 2.7→29.325 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.851 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.2236 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7445 / SU B: 15.83 / SU ML: 0.315 / SU R Cruickshank DPI: 0.6386 / SU Rfree: 0.4092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.639 / ESU R Free: 0.409 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.38 Å2 / Biso mean: 54.8343 Å2 / Biso min: 2.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.325 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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