+Open data
-Basic information
Entry | Database: PDB / ID: 4lcy | ||||||
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Title | Crystal structure of HLA-b46 at 1.6 angstrom resolution | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / antigen presenting / cell surface / HLA-B46 | ||||||
Function / homology | Function and homology information antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / neutrophil degranulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / antigen processing and presentation of peptide antigen via MHC class I / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / neutrophil degranulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / antigen processing and presentation of peptide antigen via MHC class I / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway / plasma membrane => GO:0005886 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / TAP binding / protection from natural killer cell mediated cytotoxicity / regulation of immune response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / type II interferon-mediated signaling pathway / detection of bacterium / viral process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / secretory granule membrane / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / 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 / viral capsid / Modulation by Mtb of host immune system / double-stranded RNA binding / 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 / nucleoside-triphosphate phosphatase / DAP12 signaling / MHC class II protein complex binding / protein complex oligomerization / early endosome membrane / late endosome membrane / monoatomic ion channel activity / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / intracellular iron ion homeostasis / mRNA (nucleoside-2'-O-)-methyltransferase activity / adaptive immune response / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / amyloid fibril formation / learning or memory / RNA helicase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Dengue virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Liu, J.X. | ||||||
Citation | Journal: To be Published Title: Crystal Structure Analysis of the Human Leukocyte Antigen B*46:01 Authors: Liu, J.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lcy.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lcy.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lcy_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 4lcy_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 4lcy_validation.xml.gz | 42 KB | Display | |
Data in CIF | 4lcy_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lcy ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lcy | HTTPS FTP |
-Related structure data
Related structure data | 3c9nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 31786.107 Da / Num. of mol.: 2 / Fragment: UNP residues 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: B46:01 / Gene: HLA, HLA-B, HLAB / Plasmid: pET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P30484, UniProt: P01889*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA 2 MICROGLOBULIN, CDABP0092, HDCMA22P / Plasmid: pET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1064.321 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence is one fragment of Dengue Virus 1 polyprotein. Source: (synth.) Dengue virus 1 / References: UniProt: P17763*PLUS #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF ENTITY 3 HAS IEDB ID 124151. | |
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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: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M BIS-TRIS pH 5.5, 25% POLYETHYLENE GLYCOL 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25.2 Å / Num. all: 108570 / Num. obs: 107515 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.049 / Rsym value: 0.041 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.7 / Num. unique all: 15693 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C9N Resolution: 1.6→25.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.309 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.109 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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