+Open data
-Basic information
Entry | Database: PDB / ID: 3vh8 | ||||||
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Title | KIR3DL1 in complex with HLA-B*5701 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor | ||||||
Function / homology | Function and homology information HLA-B specific inhibitory MHC class I receptor activity / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / natural killer cell mediated cytotoxicity / 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 / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / natural killer cell mediated cytotoxicity / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / antigen binding / 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 / 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 / Regulation of Complement cascade / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / B cell receptor signaling pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / defense response / 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 / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / Regulation of actin dynamics for phagocytic cup formation / 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 / FCERI mediated NF-kB activation / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / blood microparticle / intracellular iron ion homeostasis / amyloid fibril formation / Potential therapeutics for SARS Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Vivian, J.P. / Rossjohn, J. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B Authors: Vivian, J.P. / Duncan, R.C. / Berry, R. / O'Connor, G.M. / Reid, H.H. / Beddoe, T. / Gras, S. / Saunders, P.M. / Olshina, M.A. / Widjaja, J.M.L. / Harpur, C.M. / Lin, J. / Maloveste, S.M. / ...Authors: Vivian, J.P. / Duncan, R.C. / Berry, R. / O'Connor, G.M. / Reid, H.H. / Beddoe, T. / Gras, S. / Saunders, P.M. / Olshina, M.A. / Widjaja, J.M.L. / Harpur, C.M. / Lin, J. / Maloveste, S.M. / Price, D.A. / Lafont, B.A.P. / McVicar, D.W. / Clements, C.S. / Brooks, A.G. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vh8.cif.gz | 314.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vh8.ent.gz | 249.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/3vh8 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/3vh8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBEGH
#1: Protein | Mass: 31639.059 Da / Num. of mol.: 2 / Fragment: HLA-B*5701, UNP residues 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B*5701 / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, UniProt: P01889*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: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 #4: Protein | Mass: 34927.266 Da / Num. of mol.: 2 / Fragment: KIR3DL1*001, UNP residues 22-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1*001 / Plasmid: pHLSec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P43629 |
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-Protein/peptide / Sugars / Non-polymers , 3 types, 1594 molecules CF
#3: Protein/peptide | Mass: 966.109 Da / Num. of mol.: 2 / Fragment: UNP residues 93-101 / Source method: obtained synthetically / Details: synthesised peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P01834 #5: Sugar | ChemComp-NAG / #6: 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: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 16% PEG 3350, 2% tacsimate pH 5.0, 0.1M tri-sodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 136837 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2RFX and 1IM9 Resolution: 1.8→35.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.88 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.97 / ESU R: 0.152 / ESU R Free: 0.135 / Phase error: 28.86 / Stereochemistry target values: ML
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.215 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.96 Å2 / Biso mean: 29.231 Å2 / Biso min: 10.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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