+Open data
-Basic information
Entry | Database: PDB / ID: 6vq2 | ||||||
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Title | HLA-B*27:05 presenting an HIV-1 14mer peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human Leukocyte Antigen / Human Immunodeficiency Virus | ||||||
Function / homology | Function and homology information integrase activity / antigen processing and presentation of peptide antigen via MHC class I / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle ...integrase activity / antigen processing and presentation of peptide antigen via MHC class I / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / : / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / 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 / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / ER to Golgi transport vesicle membrane / 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 / protein processing / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / establishment of integrated proviral latency / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / RNA-DNA hybrid ribonuclease activity / sensory perception of smell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / peptidase activity / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / viral nucleocapsid / protein homotetramerization / symbiont-mediated suppression of host gene expression / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity / immune response Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. ...Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / Mclaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Hansjorg, S. / Van Endert, P. / Harkiolaki, M. / Iversen, A.K.N. | ||||||
Citation | Journal: Cell Rep / Year: 2022 Title: Epitope length variants balance protective immune responses and viral escape in HIV-1 infection Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, ...Authors: Pymm, P. / Tenzer, S. / Wee, E. / Weimershaus, M. / Burgevin, A. / Kollnberger, S. / Gerstoft, J. / Josephs, T.M. / Ladell, K. / McLaren, J.E. / Appay, V. / Price, D.A. / Fugger, L. / Bell, J.I. / Schild, H. / van Endert, P. / Harkiolaki, M. / Iversen, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vq2.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vq2.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/6vq2 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/6vq2 | HTTPS FTP |
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-Related structure data
Related structure data | 6vpzC 6vqdC 6vqeC 6vqyC 6vqzC 1w0vS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 31928.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: O78189 | ||||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 1744.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS | ||||
#4: Chemical | #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: 2.58 Å3/Da / Density % sol: 52.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20 %w/v Polyethylene Glycol 8000, 0.05 M Potassium di-Hydrogen Phosphate |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→66.284 Å / Num. all: 23098 / Num. obs: 23098 / % possible obs: 100 % / Redundancy: 12.4 % / Rpim(I) all: 0.129 / Rrim(I) all: 0.458 / Rsym value: 0.439 / Net I/av σ(I): 1 / Net I/σ(I): 7.8 / Num. measured all: 286507 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W0V Resolution: 2.25→55.287 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.49 Å2 / Biso mean: 28.5825 Å2 / Biso min: 5.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→55.287 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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