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Yorodumi- PDB-6la6: Cryo-EM structure of echovirus 11 complexed with its uncoating re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6la6 | ||||||
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Title | Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4 | ||||||
Components |
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Keywords | VIRUS / Cryo-EM structure / echovirus 11 / FcRn | ||||||
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 / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / T=pseudo3 icosahedral viral capsid / negative regulation of receptor binding / DAP12 interactions / 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 / regulation of erythrocyte differentiation / cytoplasmic vesicle membrane / 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 / T cell mediated cytotoxicity / endocytosis involved in viral entry into host cell / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / symbiont-mediated suppression of host gene expression / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of immune response / viral capsid / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / DAP12 signaling / MHC class II protein complex binding / protein complex oligomerization / early endosome membrane / late endosome membrane / monoatomic ion channel activity / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / DNA replication / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / RNA helicase activity / endosome membrane / symbiont entry into host cell / induction by virus of host autophagy / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Echovirus E11 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å | ||||||
Authors | Liu, S. / Gao, F.G. | ||||||
Citation | Journal: Chin.Sci.Bull. / Year: 2020 Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Authors: Niu, S. / Liu, C. / Liu, C. / Liu, S. / Song, Y. / Zhang, Y. / Tian, W. / Zhao, X. / Wang, P. / Gao, F.G. | ||||||
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 | 6la6.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6la6.ent.gz | 179.2 KB | Display | PDB format |
PDBx/mmJSON format | 6la6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6la6_validation.pdf.gz | 881 KB | Display | wwPDB validaton report |
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Full document | 6la6_full_validation.pdf.gz | 886.8 KB | Display | |
Data in XML | 6la6_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 6la6_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6la6 ftp://data.pdbj.org/pub/pdb/validation_reports/la/6la6 | HTTPS FTP |
-Related structure data
Related structure data | 0857MC 0854C 0855C 0856C 0858C 0859C 0860C 0867C 0870C 0871C 6la3C 6la4C 6la5C 6la7C 6laoC 6lapC 6lb1C 6lboC 6lbqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Capsid protein ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32277.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: Q2LJ73*PLUS |
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#2: Protein | Mass: 27968.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: A0A0R5YS56*PLUS |
#3: Protein | Mass: 26062.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: A0A346I7K2*PLUS |
#4: Protein | Mass: 7495.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: E0WN77*PLUS |
-Protein , 2 types, 2 molecules EF
#5: Protein | Mass: 29294.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCRN / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / 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 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P61769 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | 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 |
Image recording | Electron dose: 1.025 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92892 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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