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- PDB-1qvo: STRUCTURES OF HLA-A*1101 IN COMPLEX WITH IMMUNODOMINANT NONAMER A... -
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Basic information
Entry | Database: PDB / ID: 1qvo | ||||||
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Title | STRUCTURES OF HLA-A*1101 IN COMPLEX WITH IMMUNODOMINANT NONAMER AND DECAMER HIV-1 EPITOPES CLEARLY REVEAL THE PRESENCE OF A MIDDLE ANCHOR RESIDUE | ||||||
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![]() | IMMUNE SYSTEM | ||||||
Function / homology | ![]() symbiont-mediated suppression of host adaptive immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / virion component => GO:0044423 / suppression by virus of host autophagy / 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 ...symbiont-mediated suppression of host adaptive immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / virion component => GO:0044423 / suppression by virus of host autophagy / 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 / host cell Golgi membrane / 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 / 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 / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Li, L. / McNicholl, J.M. / Bouvier, M. | ||||||
![]() | ![]() Title: Structures of HLA-A*1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue. Authors: Li, L. / Bouvier, M. #1: ![]() Title: Crystallization and preliminary X-ray crystallographic studies of HLA-A*1101 complexed with an HIV-1 decapeptide Authors: Li, L. / Promadej, N. / McNicholl, J.M. / Bouvier, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 170.4 KB | Display | ![]() |
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PDB format | ![]() | 140.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 399.3 KB | Display | ![]() |
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Full document | ![]() | 417.5 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31855.051 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS ALPHA 1,ALPHA 2 AND ALPHA 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1234.509 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE PEPTIDE WAS OBTAINED THROUGH STANDARD SOLID-PHASE PEPTIDE SYNTHESIS. The sequence of the peptide is naturally found in Human Immunodeficiency Virus Type 1. Source: (synth.) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.3 Å / Num. all: 43166 / Num. obs: 40704 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.22→2.34 Å / Mean I/σ(I) obs: 2.4 / % possible all: 51.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 53.0261 Å2 / ksol: 0.453517 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→49.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.34 Å / Rfactor Rfree error: 0.025
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