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Yorodumi- PDB-1e27: Nonstandard peptide binding of HLA-B*5101 complexed with HIV immu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+27 | ||||||
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Title | Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM1(LPPVVAKEI) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA B51 / HIV / MHC CLASS I / HISTOCOMPATIBILITY COMPLEX | ||||||
Function / homology | Function and homology information : / : / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / TAP binding / protection from natural killer cell mediated cytotoxicity ...: / : / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / : / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / retroviral ribonuclease H / exoribonuclease H / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / : / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / DNA integration / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA-directed DNA polymerase / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / RNA-DNA hybrid ribonuclease activity / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / DNA recombination / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Maenaka, K. / Maenaka, T. / Tomiyama, H. / Takiguchi, M. / Stuart, D.I. / Jones, E.Y. | ||||||
Citation | Journal: J Immunol. / Year: 2000 Title: Nonstandard peptide binding revealed by crystal structures of HLA-B*5101 complexed with HIV immunodominant epitopes. Authors: Maenaka, K. / Maenaka, T. / Tomiyama, H. / Takiguchi, M. / Stuart, D.I. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e27.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e27.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 1e27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e27 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e27 | HTTPS FTP |
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-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: 32051.305 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CELL SURFACECell membrane / Plasmid: PGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P18464, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XA90 / References: UniProt: P01884, UniProt: P61769*PLUS |
#3: Protein/peptide | Mass: 966.193 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR RESIDUES 742-750 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / References: UniProt: P24740 |
#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: 2.59 Å3/Da / Density % sol: 52.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.97 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 153441 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 40.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 15.9 / % possible all: 92.7 |
Reflection | *PLUS Num. obs: 23647 / Num. measured all: 153441 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HLA B53 Resolution: 2.2→25 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Rfactor obs: 0.206 |