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- PDB-3w39: Crystal structure of HLA-B*5201 in complexed with HIV immunodomin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w39 | ||||||
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Title | Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI) | ||||||
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![]() | IMMUNE SYSTEM / Class I Major Histocompatibility Complex / MHC / Membrane | ||||||
Function / homology | ![]() antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway / plasma membrane => GO:0005886 / TAP binding / protection from natural killer cell mediated cytotoxicity / regulation of immune response / type II interferon-mediated signaling pathway / detection of bacterium / viral process / secretory granule membrane / 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 / 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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / host multivesicular body / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / DNA integration / 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 / Interferon alpha/beta signaling / 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 / iron ion transport / ER-Phagosome pathway / symbiont-mediated suppression of host gene expression / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / DNA recombination / intracellular iron ion homeostasis / adaptive immune response Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. ...Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. / Mallal, S. / John, M. / Ose, T. / Matsubara, H. / Kanda, R. / Fukunaga, Y. / Honda, K. / Kawashima, Y. / Ariumi, Y. / Oka, S. / Maenaka, K. / Takiguchi, M. | ||||||
![]() | ![]() Title: Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity Authors: Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. / Mallal, S. / John, M. / Ose, T. / Matsubara, H. ...Authors: Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. / Mallal, S. / John, M. / Ose, T. / Matsubara, H. / Kanda, R. / Fukunaga, Y. / Honda, K. / Kawashima, Y. / Ariumi, Y. / Oka, S. / Maenaka, K. / Takiguchi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.5 KB | Display | ![]() |
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PDB format | ![]() | 129.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.7 KB | Display | ![]() |
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Full document | ![]() | 492.5 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e28S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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Components
#1: Protein | Mass: 32137.414 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR RESIDUES 25-300 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: 848.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic HIV-1 PEPTIDE Source: (synth.) ![]() References: UniProt: P12499 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 31, 2012 / Details: mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→46.9 Å / Num. all: 18422 / Num. obs: 18422 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 23.07 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2548 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.02 Å2 / Biso mean: 14.3983 Å2 / Biso min: 4.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→38.802 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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