+Open data
-Basic information
Entry | Database: PDB / ID: 3wuw | ||||||
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Title | KIR3DL1 in complex with HLA-B*57:01.I80T | ||||||
Components |
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Keywords | PROTEIN BINDING / Immune receptor complex | ||||||
Function / homology | Function and homology information HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / natural killer cell mediated cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / TAP binding / FCGR activation / protection from natural killer cell mediated cytotoxicity / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / detection of bacterium / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / Regulation of Complement cascade / antigen binding / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / 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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / Regulation of actin dynamics for phagocytic cup formation / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / FCERI mediated NF-kB activation / 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 / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response Similarity search - Function | ||||||
Biological species | Homo sapiens (human) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Vivian, J.P. / Rossjohn, J. | ||||||
Citation | Journal: J.Immunol. / Year: 2014 Title: Mutational and structural analysis of KIR3DL1 reveals a lineage-defining allotypic dimorphism that impacts both HLA and peptide sensitivity Authors: O'connor, G.M. / Vivian, J.P. / Widjaja, J.M. / Bridgeman, J.S. / Gostick, E. / Lafont, B.A.P. / Anderson, S.K. / Price, D.A. / Brooks, A.G. / Rossjohn, J. / Mcvicar, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wuw.cif.gz | 162.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wuw.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/3wuw ftp://data.pdbj.org/pub/pdb/validation_reports/wu/3wuw | HTTPS FTP |
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-Related structure data
Related structure data | 3vh8S S: Starting model for refinement |
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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: 31627.004 Da / Num. of mol.: 1 Fragment: HLA-B*57:01 extracellular domain, UNP residues 25-299 Mutation: I80T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-B*57:01, HLAB / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P18465, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11635.002 Da / Num. of mol.: 1 / Fragment: Beta 2 Microglobulin, UNP residues 22-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, Beta 2 Microglobulin, CDABP0092, HDCMA22P / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#4: Protein | Mass: 33513.816 Da / Num. of mol.: 1 Fragment: KIR3DL1*001 extracellular domains, UNP residues 28-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD158E, KIR3DL1, KIR3DL1*001, NKAT3, NKB1 / Plasmid: pHLSec / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P43629 |
-Protein/peptide / Sugars / Non-polymers , 3 types, 497 molecules C
#3: Protein/peptide | Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesised peptide / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01834*PLUS | ||
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#5: Sugar | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE SEQUENCE OF THE ENTITY3 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ...THE SEQUENCE OF THE ENTITY3 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
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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: 2.53 Å3/Da / Density % sol: 51.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG3350, 2% tacsimate(pH 5.0), 0.1M tri-sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9546 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9546 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.472 Å / Num. obs: 49831 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7177 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VH8 Resolution: 2→40 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.55 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.656 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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