+Open data
-Basic information
Entry | Database: PDB / ID: 6v2p | ||||||
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Title | HLA-B*57:03 presenting the peptide ASLNLPAVSW | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Peptide Antigen / HLA / MHC / Immunity | ||||||
Function / homology | Function and homology information negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / cellular response to indole-3-methanol / vinculin binding ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / cellular response to indole-3-methanol / vinculin binding / flotillin complex / negative regulation of cell motility / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / catenin complex / negative regulation of protein localization to nucleus / antigen processing and presentation of peptide antigen via MHC class I / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / Myogenesis / odontogenesis of dentin-containing tooth / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intercalated disc / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / VEGFR2 mediated vascular permeability / 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 / integrin-mediated signaling pathway / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / adherens junction / 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 / protein localization / 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 / cell-cell adhesion / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / beta-catenin binding / 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 / response to estrogen / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / male gonad development / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / cell migration / actin filament binding / cell-cell junction / sensory perception of smell / actin cytoskeleton / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / cell junction / lamellipodium / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Maclachlan, B. / Rossjohn, J. / Vivian, J.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function. Authors: Saunders, P.M. / MacLachlan, B.J. / Pymm, P. / Illing, P.T. / Deng, Y. / Wong, S.C. / Oates, C.V.L. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P. / Brooks, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v2p.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v2p.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/6v2p ftp://data.pdbj.org/pub/pdb/validation_reports/v2/6v2p | HTTPS FTP |
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-Related structure data
Related structure data | 6v2oC 6v2qC 6v3jC 2rfxS 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31811.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: I3ZN84 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1057.200 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) / References: UniProt: P35221*PLUS |
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-Non-polymers , 3 types, 529 molecules
#4: Chemical | ChemComp-PEG / |
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#5: Chemical | ChemComp-ACT / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 20 % PEG 4000, 0.2 M ammonium acetate, 0.1 M tri-sodium citrate pH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→46.32 Å / Num. obs: 115263 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5638 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RFX Resolution: 1.3→41.139 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→41.139 Å
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Refine LS restraints |
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LS refinement shell |
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