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Yorodumi- PDB-6pz5: Crystal Structure of HLA-B*2703 in complex with LRN, a self-peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pz5 | ||||||
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Title | Crystal Structure of HLA-B*2703 in complex with LRN, a self-peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ankylosing spondylitis / HLA-B27 / HLA-B*27:05 / HLA-B*27:03 / HLA | ||||||
Function / homology | Function and homology information squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / regulation of interleukin-12 production / regulation of dendritic cell differentiation / ergosterol biosynthetic process ...squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / regulation of interleukin-12 production / regulation of dendritic cell differentiation / ergosterol biosynthetic process / regulation of T cell anergy / regulation of interleukin-6 production / cholesterol biosynthetic process / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / Activation of gene expression by SREBF (SREBP) / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / PPARA activates gene expression / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / positive regulation of cellular senescence / peptide antigen binding / 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 / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å | ||||||
Authors | Gras, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Allelic association with ankylosing spondylitis fails to correlate with human leukocyte antigen B27 homodimer formation. Authors: Lim Kam Sian, T.C.C. / Indumathy, S. / Halim, H. / Greule, A. / Cryle, M.J. / Bowness, P. / Rossjohn, J. / Gras, S. / Purcell, A.W. / Schittenhelm, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pz5.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pz5.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 6pz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pz5_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 6pz5_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 6pz5_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6pz5_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/6pz5 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/6pz5 | HTTPS FTP |
-Related structure data
Related structure data | 6pyjC 6pylC 6pyvC 6pywC 4g9dS 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
#1: Protein | Mass: 31903.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P03989, 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 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1125.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P37268*PLUS |
#4: Water | ChemComp-HOH / |
Sequence details | Y83H IN ALLELE B*27:03 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20-30% PEG 4K, 0.2M Na Acetate and 0.1M Na 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: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→46.28 Å / Num. obs: 82863 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 17.44 Å2 / Rpim(I) all: 0.039 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.53→1.56 Å / Num. unique obs: 19314 / Rpim(I) all: 0.339 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4g9d Resolution: 1.53→41.26 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.079
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Displacement parameters | Biso max: 104.82 Å2 / Biso mean: 21.25 Å2 / Biso min: 6.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→41.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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