+Open data
-Basic information
Entry | Database: PDB / ID: 5b38 | ||||||
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Title | KIR3DL1*005 in complex with HLA-B*57:01 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Innate Immune Receptor / KIR / Natural Killer Cell | ||||||
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 / 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 / Regulation of Complement cascade / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCGR3A-mediated phagocytosis / 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 / negative regulation of forebrain neuron differentiation / defense response / 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 / 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 / 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 / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Vivian, J.P. / Rossjohn, J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Exp.Med. / Year: 2016 Title: Killer cell immunoglobulin-like receptor 3DL1 polymorphism defines distinct hierarchies of HLA class I recognition Authors: Saunders, P.M. / Pymm, P. / Pietra, G. / Hughes, V.A. / Hitchen, C. / O'Connor, G.M. / Loiacono, F. / Widjaja, J. / Price, D.A. / Falco, M. / Mingari, M.C. / Moretta, L. / McVicar, D.W. / ...Authors: Saunders, P.M. / Pymm, P. / Pietra, G. / Hughes, V.A. / Hitchen, C. / O'Connor, G.M. / Loiacono, F. / Widjaja, J. / Price, D.A. / Falco, M. / Mingari, M.C. / Moretta, L. / McVicar, D.W. / Rossjohn, J. / Brooks, A.G. / Vivian, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b38.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b38.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 5b38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/5b38 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/5b38 | HTTPS FTP |
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-Related structure data
Related structure data | 5b39C 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: 31736.172 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P18465, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P61769 |
#4: Protein | Mass: 32993.367 Da / Num. of mol.: 1 / Fragment: UNP residues 22-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P43629 |
-Protein/peptide / Sugars / Non-polymers , 3 types, 239 molecules C
#3: Protein/peptide | Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01834 | ||
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#5: Sugar | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14 to 18% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 61910 / % possible obs: 92.9 % / Redundancy: 4.5 % / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.3→2.42 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VH8 Resolution: 2.3→35.496 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.65 / Phase error: 28.13 Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35.496 Å
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Refine LS restraints |
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LS refinement shell |
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