+Open data
-Basic information
Entry | Database: PDB / ID: 4g9f | ||||||
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Title | Crystal Structure of C12C TCR-HLAB2705-KK10-L6M | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR / T cell / HLA B*2705 / KK10 / KK10-L6M / HIV / immune escape | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / viral process ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / viral process / 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 / viral capsid / 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 / 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 / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity / immune response / symbiont entry into host cell / Amyloid fiber formation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Gras, S. / Wilmann, P.G. / Rossjohn, J. | ||||||
Citation | Journal: Immunity / Year: 2013 Title: A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8(+) T Cells. Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. ...Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. / Agut, H. / van Bockel, D.J. / Almeida, J.R. / Douek, D.C. / Meyer, L. / Venet, A. / Takiguchi, M. / Rossjohn, J. / Price, D.A. / Appay, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g9f.cif.gz | 191.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g9f.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 4g9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/4g9f ftp://data.pdbj.org/pub/pdb/validation_reports/g9/4g9f | 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
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03989, UniProt: P01889*PLUS |
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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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
#4: Protein | Mass: 23086.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
#5: Protein | Mass: 27822.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1261.602 Da / Num. of mol.: 1 / Fragment: UNP residues 22-31 / Source method: obtained synthetically / Details: from manufacturer / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YNZ1, UniProt: P03366*PLUS |
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-Non-polymers , 2 types, 489 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG 8000 and 0.1M MES, pH 7, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. obs: 68882 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.87 Å2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Resolution: 1.9→59.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.8999 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.221 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→59.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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