+Open data
-Basic information
Entry | Database: PDB / ID: 6j1v | ||||||
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Title | The structure of HLA-A*3003/RT313 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / The structure of HLA-A*3003/RT313 | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / antigen processing and presentation / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / HIV-1 retropepsin / 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 / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / 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 / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / protein processing / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / 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 / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / specific granule lumen / recycling endosome membrane / RNA stem-loop binding / 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 / RNA-directed DNA polymerase activity / positive regulation of immune response / Modulation by Mtb of host immune system / host cell / RNA-DNA hybrid ribonuclease activity / sensory perception of smell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / peptidase activity / iron ion transport / ER-Phagosome pathway / symbiont-mediated suppression of host gene expression / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity / symbiont entry into host cell Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Zhu, S.Y. / Liu, K.F. / Chai, Y. / Ding, C.M. / Lv, J.X. / Gao, G.F. / Lou, Y.L. / Liu, W.J. | ||||||
Citation | Journal: Front Immunol / Year: 2019 Title: Divergent Peptide Presentations of HLA-A*30 Alleles Revealed by Structures With Pathogen Peptides. Authors: Zhu, S. / Liu, K. / Chai, Y. / Wu, Y. / Lu, D. / Xiao, W. / Cheng, H. / Zhao, Y. / Ding, C. / Lyu, J. / Lou, Y. / Gao, G.F. / Liu, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j1v.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j1v.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 6j1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j1v_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 6j1v_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 6j1v_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6j1v_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/6j1v ftp://data.pdbj.org/pub/pdb/validation_reports/j1/6j1v | HTTPS FTP |
-Related 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: 31592.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A173ADK6*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) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1013.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*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: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 25% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: SDMS / Detector: IMAGE PLATE / Date: Jan 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 32751 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 0.2 |
Reflection shell | Resolution: 2→2.07 Å |
-Processing
Software |
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Refinement | Resolution: 2→48.2 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.2 Å
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Refine LS restraints |
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LS refinement shell |
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