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Yorodumi- PDB-3bp7: The high resolution crystal structure of HLA-B*2709 in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 3bp7 | ||||||
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Title | The high resolution crystal structure of HLA-B*2709 in complex with a Cathepsin A signal sequence peptide, pCatA | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / HLA-B*2709 / HLA-B2709 / beta-2-microglobulin / b2m / Cathepsin A signal sequence / pCatA / Ankylosing Spondylitis / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Carboxypeptidase / Hydrolase / Lysosome / Protease / Zymogen | ||||||
Function / homology | Function and homology information carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / regulation of chaperone-mediated autophagy / Sialic acid metabolism / Glycosphingolipid catabolism / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / negative regulation of chaperone-mediated autophagy ...carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / regulation of chaperone-mediated autophagy / Sialic acid metabolism / Glycosphingolipid catabolism / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / negative regulation of chaperone-mediated autophagy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation / lysosomal lumen / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / intracellular protein transport / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 protein stability / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / 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 / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / lysosome / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Homo Sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Merino, E. / Lopez de Castro, J.A. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bp7.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bp7.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bp7_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 3bp7_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 3bp7_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 3bp7_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bp7 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bp7 | HTTPS FTP |
-Related structure data
Related structure data | 3bp4C 3bvnC 3bxnC 1jgeS C: citing same article (ref.) 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
#1: Protein | Mass: 31951.219 Da / Num. of mol.: 1 Fragment: HLA-B*2709 extracellular domain, UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03989, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 982.198 Da / Num. of mol.: 1 / Fragment: Cathepsin A signal sequence, UNP residues 2-10 / Source method: obtained synthetically Details: Cathepsin A signal sequence peptide, pCatA, chemically synthesized, This sequence occurs naturally in humans. Source: (synth.) Homo Sapiens (human) / References: UniProt: P10619 |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | THE 140TH RESIDUE IS HIS IN ALLELE B*2709. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 23.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 18, 2006 / Details: Mirrors |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 41600 / % possible obs: 93.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.796 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.07 / Num. unique all: 3694 / Χ2: 0.684 / % possible all: 84.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.47 / Cor.coef. Fo:Fc: 0.463
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JGE Resolution: 1.8→46.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.24 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.117 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.797→1.843 Å / Total num. of bins used: 20
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