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- PDB-1t1y: Structural basis for degenerate recognition of HIV peptide varian... -
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Basic information
Entry | Database: PDB / ID: 1t1y | ||||||
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Title | Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-5V | ||||||
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![]() | IMMUNE SYSTEM / CTL / CYTOTOXIC T LYMPHOCYTES / HIV / HUMAN IMMUNODEFICIENCY VIRUS / MHC / MAJOR HISTOCOMPATIBILITY COMPLEX / PMHC / PEPTIDE MHC COMPLEX / RMSD / ROOT-MEAN-SQUARED DEVIATION / SIV / SIMIAN IMMUNODEFICIENCY VIRUS / TCR / T-CELL RECEPTOR | ||||||
Function / homology | ![]() : / : / regulation of membrane depolarization / retina homeostasis / 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 / Golgi medial cisterna ...: / : / regulation of membrane depolarization / retina homeostasis / 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 / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez-Hackert, E. / Anikeeva, N. / Kalams, S.A. / Walker, B.D. / Hendrickson, W.A. / Sykulev, Y. | ||||||
![]() | ![]() Title: Structural Basis for Degenerate Recognition of Natural HIV Peptide Variants by Cytotoxic Lymphocytes. Authors: Martinez-Hackert, E. / Anikeeva, N. / Kalams, S.A. / Walker, B.D. / Hendrickson, W.A. / Sykulev, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.1 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1s8dC ![]() 1t1wC ![]() 1t1xC ![]() 1t1zC ![]() 1t20C ![]() 1t21C ![]() 1t22C ![]() 2hlaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 1 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 979.128 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human immunodeficiency virus. |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG, MES, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 28488 / Biso Wilson estimate: 11.1 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HLA Resolution: 2→11.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1499169.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.1278 Å2 / ksol: 0.453413 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→11.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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