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Yorodumi- PDB-6v3j: KIR3DL1 in complex with HLA-B*57:03 presenting the peptide LSSPVTKSF -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v3j | ||||||
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Title | KIR3DL1 in complex with HLA-B*57:03 presenting the peptide LSSPVTKSF | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Peptide Antigen / HLA / MHC / Immunity | ||||||
Function / homology | Function and homology information HLA-B specific inhibitory MHC class I receptor activity / natural killer cell mediated cytotoxicity / antigen processing and presentation of peptide antigen via MHC class I / 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 ...HLA-B specific inhibitory MHC class I receptor activity / natural killer cell mediated cytotoxicity / antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / 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 / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / 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 / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / molecular adaptor activity / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 | 6v3j.cif.gz | 162.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v3j.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 6v3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/6v3j ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v3j | HTTPS FTP |
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-Related structure data
Related structure data | 6v2oC 6v2pC 6v2qC 3vh8S 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 , 3 types, 3 molecules ABG
#1: Protein | Mass: 31714.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-B*5703GB / 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 |
#4: Protein | Mass: 33076.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Variant: *001 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P43629 |
-Protein/peptide / Sugars / Non-polymers , 3 types, 403 molecules C
#3: Protein/peptide | Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#5: Sugar | #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: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14% PEG 3350, 2% tacsimate, pH 5.0, 0.1 M tri-sodium citrate pH 5.6 |
-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: Aug 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.975→50 Å / Num. obs: 50170 / % possible obs: 97.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.98→2.08 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7050 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VH8 Resolution: 1.98→48.107 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.45 Å2 / Biso mean: 40.6068 Å2 / Biso min: 17.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→48.107 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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