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Yorodumi- PDB-3hcv: Crystal structure of HLA-B*2709 complexed with the double citrull... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hcv | |||||||||
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Title | Crystal structure of HLA-B*2709 complexed with the double citrullinated vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) I / HLA-B*2709 / GLYCOPROTEIN / HOST-VIRUS / IMMUNE RESPONSE / POLYMORPHISM / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / MEMBRANE / TRANSMEMBRANE / UBL CONJUGATION / DISEASE MUTATION / GLYCATION / PYRROLIDONE CARBOXYLIC ACID / SECRETED / Disulfide bond / MHC I | |||||||||
Function / homology | Function and homology information vasoactive intestinal polypeptide receptor activity / regulation of interleukin-12 production / G protein-coupled peptide receptor activity / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding / protection from natural killer cell mediated cytotoxicity ...vasoactive intestinal polypeptide receptor activity / regulation of interleukin-12 production / G protein-coupled peptide receptor activity / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / 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 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / Glucagon-type ligand receptors / 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 / 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 / G alpha (s) signalling events / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / receptor complex / learning or memory / cell surface receptor signaling pathway / immune response / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Beltrami, A. / Gabdulkhakov, A. / Rossmann, M. / Ziegler, A. / Uchanska-Ziegler, B. / Saenger, W. | |||||||||
Citation | Journal: To be Published Title: Citrullination-and mhc polymorphism-dependent conformational changes of a self peptide Authors: Beltrami, A. / Rossmann, M. / Gabdulkhakov, A. / Ziegler, A. / Uchanska-Ziegler, B. / Saenger, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hcv.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hcv.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hcv_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 3hcv_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 3hcv_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 3hcv_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hcv ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hcv | HTTPS FTP |
-Related structure data
Related structure data | 3dtxC 1ogtS 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: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLUAR DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1399.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / References: UniProt: P32241*PLUS |
#4: 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: 2.93 Å3/Da / Density % sol: 58.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M TRIS HCL,25% PEG 8000, , pH 8.000000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.982 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.982 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 48072 / Num. obs: 39804 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.49 / Num. unique all: 2914 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ogt Resolution: 1.95→48.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.227 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.809 / SU B: 8.565 / SU ML: 0.109 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.173 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.24 Å2 / Biso mean: 19.765 Å2 / Biso min: 6.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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