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Yorodumi- PDB-3mrh: Crystal Structure of MHC class I HLA-A2 molecule complexed with H... -
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-Basic information
Entry | Database: PDB / ID: 3mrh | ||||||
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Title | Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide N3S variant | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I / HLA / IMMUNE RESPONSE / NONAPEPTIDE / VIRAL PEPTIDE / HEPATITIS C VIRUS / NS3 PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of triglyceride biosynthetic process / hepacivirin / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / host cell mitochondrial membrane / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...positive regulation of triglyceride biosynthetic process / hepacivirin / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / host cell mitochondrial membrane / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / host cell lipid droplet / CD8 receptor binding / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / antigen processing and presentation of exogenous peptide antigen via MHC class I / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / SH3 domain binding / 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 / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / protein complex oligomerization / late endosome membrane / monoatomic ion channel activity / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / learning or memory Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hepatitis C virus genotype 1b | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gras, S. / Reiser, J.-B. / Chouquet, A. / Le Gorrec, M. / Debeaupuis, E. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / Housset, D. | ||||||
Citation | Journal: J.Immunol. / Year: 2014 Title: Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans. Authors: Reiser, J.B. / Legoux, F. / Gras, S. / Trudel, E. / Chouquet, A. / Leger, A. / Le Gorrec, M. / Machillot, P. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mrh.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mrh.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mrh_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 3mrh_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 3mrh_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3mrh_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/3mrh ftp://data.pdbj.org/pub/pdb/validation_reports/mr/3mrh | HTTPS FTP |
-Related structure data
Related structure data | 3mrcC 3mrdC 3mreC 3mrgSC 3mrlC 3mroC 3mrrC 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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Unit cell |
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-Components
#1: Protein | Mass: 34008.711 Da / Num. of mol.: 1 / Fragment: HLA-A*0201 alpha chain, UNP resiude 25-300 / Mutation: A245V Source method: isolated from a genetically manipulated source Details: C-terminal biotin acceptor peptide sequence tag (GSLHHILDAQKMVWNHR) Source: (gene. exp.) Homo sapiens (human) / Gene: HLA, HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LAQQ1 / References: UniProt: P01892, UniProt: P04439*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) / Gene: B2M, BETA-2 MICROGLUBULIN, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LAQQ1 / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 967.163 Da / Num. of mol.: 1 / Fragment: NS3 protein fragment, UNP residues 1073-1081 / Mutation: N3S / Source method: obtained synthetically Details: chemical synthesis; Variant of a sequence occurring in Hepatitis C virus NS3 protein Source: (synth.) Hepatitis C virus genotype 1b (isolate HC-J1) References: UniProt: Q03463 |
#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: 2.36 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9% PEG 6000, 0.1M NaCitrate, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 17070 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 46.576 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MRG Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.856 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. ...Details: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds to the coordinates just before these very last cycles.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.22 Å2 / Biso mean: 45.077 Å2 / Biso min: 17.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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