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Open data
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Basic information
Entry | Database: PDB / ID: 4g9d | ||||||
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Title | Crystal Structure of HLA B2705-KK10 | ||||||
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![]() | IMMUNE SYSTEM / TCR / T cell / HLA B*2705 / KK10 / KK10-L6M / HIV / immune escape | ||||||
Function / homology | ![]() regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / viral process / RNA-directed DNA polymerase activity ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / viral process / RNA-directed DNA polymerase activity / detection of bacterium / : / : / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / peptide antigen assembly with MHC class II protein complex / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / cellular response to iron(III) ion / exoribonuclease H / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / exoribonuclease H activity / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / 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 / host multivesicular body / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / DNA integration / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / specific granule lumen / viral penetration into host nucleus / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / Interferon alpha/beta signaling / MHC class II protein complex binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / tertiary granule lumen / DAP12 signaling / host cell / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / adaptive immune response / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / learning or memory / immune response Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gras, S. / Wilmann, P.G. / Rossjohn, J. | ||||||
![]() | ![]() Title: A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8(+) T Cells. Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. ...Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. / Agut, H. / van Bockel, D.J. / Almeida, J.R. / Douek, D.C. / Meyer, L. / Venet, A. / Takiguchi, M. / Rossjohn, J. / Price, D.A. / Appay, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | 81.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4g8gC ![]() 4g8iC ![]() 4g9fC ![]() 1ogtS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1243.564 Da / Num. of mol.: 1 / Fragment: UNP residues 99-108 / Source method: obtained synthetically / Details: GL peptide / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24% PEG 3350 and 0.3M Na2SO4, pH 8, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 61797 / % possible obs: 100 % / Redundancy: 7.1 % |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ogt Resolution: 1.6→46.366 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 23.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3221 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→46.366 Å
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Refine LS restraints |
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LS refinement shell |
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