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Yorodumi- EMDB-53923: Structure of the Human Peptide-Loading Complex Arrested by HCMV US6 -
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Open data
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Basic information
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| Title | Structure of the Human Peptide-Loading Complex Arrested by HCMV US6 | ||||||||||||||||||
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Keywords | antigen processing / adaptive immunity / cryo-EM / ER chaperones / MHC class I / transporter associated with antigen processing / IMMUNE SYSTEM | ||||||||||||||||||
| Function / homology | Function and homology informationMHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity / TAP2 binding / TAP1 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / peptide transport / peptide transmembrane transporter activity / TAP complex binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / molecular sequestering activity / antigen processing and presentation of peptide antigen via MHC class I / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / defense response / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / transmembrane transport / centriolar satellite / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / unfolded protein binding / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / protein transport / negative regulation of neuron projection development / ER-Phagosome pathway / regulation of gene expression / protein refolding / protein-containing complex assembly / early endosome membrane / protein homotetramerization / amyloid fibril formation / molecular adaptor activity / adaptive immune response / intracellular iron ion homeostasis / learning or memory / nuclear speck / immune response / host cell endoplasmic reticulum membrane / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane Similarity search - Function | ||||||||||||||||||
| Biological species | Homo sapiens (human) | ||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
Authors | Stolz M / Susac L / Trowitzsch S / Tampe R | ||||||||||||||||||
| Funding support | European Union, Germany, United States, 5 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||||||||||||||
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_53923.map.gz | 472.5 MB | EMDB map data format | |
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| Header (meta data) | emd-53923-v30.xml emd-53923.xml | 27.9 KB 27.9 KB | Display Display | EMDB header |
| Images | emd_53923.png | 73.2 KB | ||
| Filedesc metadata | emd-53923.cif.gz | 9 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-53923 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-53923 | HTTPS FTP |
-Validation report
| Summary document | emd_53923_validation.pdf.gz | 523.9 KB | Display | EMDB validaton report |
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| Full document | emd_53923_full_validation.pdf.gz | 523.5 KB | Display | |
| Data in XML | emd_53923_validation.xml.gz | 8 KB | Display | |
| Data in CIF | emd_53923_validation.cif.gz | 9.3 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-53923 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-53923 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9rcvMC ![]() 53326 ![]() 53330 ![]() 53331 ![]() 53332 ![]() 53334 M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_53923.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Human peptide-loading complex arrested by HCMV US6
+Supramolecule #1: Human peptide-loading complex arrested by HCMV US6
+Macromolecule #1: Antigen peptide transporter 1
+Macromolecule #2: Tapasin
+Macromolecule #3: MHC class I antigen
+Macromolecule #4: Beta-2-microglobulin
+Macromolecule #5: Antigen peptide transporter 2
+Macromolecule #6: Unique short US6 glycoprotein
+Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #12: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 3.5 mg/mL | ||||||||||||||||||
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| Buffer | pH: 6.5 Component:
Details: 20 mM HEPES-NaOH pH 6.5, 150 mM NaCl, 10 mM MgCl2, 2.5 mM biotin, 0.05% (w/v) glycodiosgenin | ||||||||||||||||||
| Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 5, Blot time 5 s. |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 25454 / Average electron dose: 58.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Calibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Germany,
United States, 5 items
Citation







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Y (Row.)
X (Col.)
























Processing
FIELD EMISSION GUN
