+Open data
-Basic information
Entry | Database: PDB / ID: 6vqz | ||||||
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Title | HLA-B*27:05 presenting an HIV-1 6mer peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human Leukocyte Antigen / Human Immunodeficiency Virus | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 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 / Assembly Of The HIV Virion / 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 / Budding and maturation of HIV virion / 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 / protein processing / 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 / 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 / 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 / peptidase activity / iron ion transport / ER-Phagosome pathway / symbiont-mediated suppression of host gene expression / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity 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 | 6vqz.cif.gz | 177.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vqz.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vqz_validation.pdf.gz | 265 KB | Display | wwPDB validaton report |
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Full document | 6vqz_full_validation.pdf.gz | 265 KB | Display | |
Data in XML | 6vqz_validation.xml.gz | 1.2 KB | Display | |
Data in CIF | 6vqz_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/6vqz ftp://data.pdbj.org/pub/pdb/validation_reports/vq/6vqz | HTTPS FTP |
-Related structure data
Related structure data | 6vpzC 6vq2C 6vqdC 6vqeC 6vqyC 1w0vS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 31928.160 Da / Num. of mol.: 2 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 #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 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: 830.072 Da / Num. of mol.: 2 / 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 | |
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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: 2.91 Å3/Da / Density % sol: 57.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2012 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection twin | Operator: h,-k,-h-l / Fraction: 0.44 | |||||||||||||||||||||
Reflection | Resolution: 2.25→130.49 Å / Num. obs: 47317 / % possible obs: 98.1 % / Redundancy: 2.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.7 | |||||||||||||||||||||
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→87.333 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.88 / Stereochemistry target values: TWIN_LSQ_F
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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 max: 192.77 Å2 / Biso mean: 38.2333 Å2 / Biso min: 11.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→87.333 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 / Rfactor Rfree error: 0 / Total num. of bins used: 16
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