+Open data
-Basic information
Entry | Database: PDB / ID: 7b5f | ||||||
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Title | Structure of echovirus 18 in complex with neonatal Fc receptor | ||||||
Components |
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Keywords | VIRUS / complex / echovirus 18 virion / neonatal fc receptor / fcrn / beta-2-microglobulin / microglobulin / pocket factor | ||||||
Function / homology | Function and homology information IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / T=pseudo3 icosahedral viral capsid / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / host cell cytoplasmic vesicle membrane / 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 / cytoplasmic vesicle membrane / 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 / HFE-transferrin receptor complex / endocytosis involved in viral entry into host cell / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / channel activity / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / monoatomic ion transmembrane transport / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / DNA replication / RNA helicase activity / learning or memory / endosome membrane / induction by virus of host autophagy / immune response / RNA-directed RNA polymerase / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / viral RNA genome replication / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / Neutrophil degranulation / host cell nucleus / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Echovirus E18 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Buchta, D. / Levdansky, Y. / Fuzik, T. / Mukhamedova, L. / Moravcova, J. / Hrebik, D. / Andersen, J.T. / Plevka, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: To Be Published Title: Structure of echovirus 18 in complex with neonatal Fc receptor Authors: Buchta, D. / Levdansky, Y. / Fuzik, T. / Mukhamedova, L. / Moravcova, J. / Hrebik, D. / Andersen, J.T. / Plevka, P. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7b5f.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b5f.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 7b5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b5f_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7b5f_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7b5f_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 7b5f_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5f ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5f | HTTPS FTP |
-Related structure data
Related structure data | 12028MC M: map data used to model this data 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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-Components
-Echovirus 18 viral protein ... , 4 types, 4 molecules CDAB
#1: Protein | Mass: 26143.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Tissue: Kidney References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Protein | Mass: 7475.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Organ: Kidney References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: Protein | Mass: 32564.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Tissue: Kidney References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: Protein | Mass: 28802.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Tissue: Kidney References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
-Protein , 2 types, 2 molecules GH
#5: Protein | Mass: 29720.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Cell line (production host): High Five cells / Production host: unidentified baculovirus / References: UniProt: P55899 |
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#6: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): High Five cells / Production host: unidentified baculovirus / References: UniProt: P61769 |
-Non-polymers , 2 types, 2 molecules
#7: Chemical | ChemComp-PLM / |
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#8: Chemical | ChemComp-GUN / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) | Organism: unidentified baculovirus | ||||||||||||||||||||||||||||||
Natural host | Organism: homo sapiens / Strain: echovirus 18 | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.3 Details: Mixed in 1:1 volume ratio {20 mM Tris (pH=7.2), 100 mM NaCl} and {8 mM Na2HPO4, 2 mM KH2PO4 (pH=7.4), 137 mM NaCl, 2.7 mM KCl}=PBS | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.27 sec. / Electron dose: 54.48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 4531 / Details: Images were collected in movie-mode at 50 frames. |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-Processing
Software | Name: PHENIX / Version: (1.13_2992: ???) / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 125031 | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13062 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Method: flexible fit / Target criteria: R-factors | ||||||||||||||||||||||||
Refinement | Resolution: 2.9→233.42 Å / SU ML: 0.65 / σ(F): 0.13 / Phase error: 34.06 / 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 | ||||||||||||||||||||||||
Refine LS restraints |
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