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Yorodumi- PDB-7sig: Crystal Structure of HLA B*3501 in complex with NPDIVIYQY, an 9-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sig | ||||||
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Title | Crystal Structure of HLA B*3501 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA B*3501 / HIV / TCR / T cell / viral peptide | ||||||
Function / homology | Function and homology information 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 ...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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / 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 / 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 / host multivesicular body / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / DNA integration / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / viral genome integration into host DNA / RNA-directed DNA polymerase / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / viral penetration into host nucleus / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / symbiont-mediated suppression of host gene expression / 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 / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / host cell / positive regulation of T cell activation / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / focal adhesion / signaling receptor binding / lipid binding / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.741 Å | ||||||
Authors | Gras, S. / Lobos, C.A. / Chatzileontiadou, D.S.M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Immunol.Cell.Biol. / Year: 2024 Title: Molecular insights into the HLA-B35 molecules' classification associated with HIV control. Authors: Lobos, C.A. / Chatzileontiadou, D.S. / Sok, B. / Almedia, C.A. / Halim, H. / D'Orsogna, L. / Gras, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sig.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sig.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 7sig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/7sig ftp://data.pdbj.org/pub/pdb/validation_reports/si/7sig | HTTPS FTP |
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-Related structure data
Related structure data | 7sifC 7sihC 4lnrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31940.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4NBT2 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1124.243 Da / Num. of mol.: 1 / Fragment: UNP residues 774-782 / Source method: obtained synthetically / Details: peptide from HIV / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03366 |
#4: Chemical | ChemComp-FLC / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % / Mosaicity: 0.17 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M Ammonium Acetate, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.74→45.56 Å / Num. obs: 40150 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 29.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.026 / Rrim(I) all: 0.06 / Net I/σ(I): 13.4 / Num. measured all: 209488 / Scaling rejects: 31 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lnr Resolution: 1.741→45.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.114
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Displacement parameters | Biso max: 72.86 Å2 / Biso mean: 31.77 Å2 / Biso min: 12.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.741→45.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.741→1.75 Å / Rfactor Rfree error: 0
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