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Yorodumi- EMDB-9687: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9687 | |||||||||
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Title | Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4 | |||||||||
Map data | Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at ph 7.4 | |||||||||
Sample |
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Function / homology | Function and homology information IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / 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 / negative regulation of receptor binding / DAP12 interactions ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / 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 / 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 / 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 / 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 / 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 / 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 / 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 / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Echovirus E6 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Gao GF / Liu S / Zhao X / Peng R | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell / Year: 2019 Title: Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B. Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / ...Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / Yan Li / Meifan Zhang / Jianxun Qi / Han Wang / Ning Du / Yan Wu / Yuhai Bi / Shan Gao / Yi Shi / Jinghua Yan / Yong Zhang / Zhengde Xie / Wensheng Wei / George F Gao / Abstract: Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for ...Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for coxsackievirus B in EV-B have been identified, receptors mediating virus entry, especially the uncoating process of echovirus and other EV-B remain obscure. Here, we found that human neonatal Fc receptor (FcRn) is the uncoating receptor for major EV-B. FcRn binds to the virus particles in the "canyon" through its FCGRT subunit. By obtaining multiple cryo-electron microscopy structures at different stages of virus entry at atomic or near-atomic resolution, we deciphered the underlying mechanisms of enterovirus attachment and uncoating. These structures revealed that different from the attachment receptor CD55, binding of FcRn to the virions induces efficient release of "pocket factor" under acidic conditions and initiates the conformational changes in viral particle, providing a structural basis for understanding the mechanisms of enterovirus entry. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9687.map.gz | 48.3 MB | EMDB map data format | |
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Header (meta data) | emd-9687-v30.xml emd-9687.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9687_fsc.xml | 14 KB | Display | FSC data file |
Images | emd_9687.png | 243.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9687 | HTTPS FTP |
-Validation report
Summary document | emd_9687_validation.pdf.gz | 405.7 KB | Display | EMDB validaton report |
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Full document | emd_9687_full_validation.pdf.gz | 405.2 KB | Display | |
Data in XML | emd_9687_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_9687_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9687 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9687 | HTTPS FTP |
-Related structure data
Related structure data | 6ilmMC 9684C 9685C 9686C 9688C 9689C 9690C 6iljC 6ilkC 6illC 6ilnC 6iloC 6ilpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9687.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at ph 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Cryo-EM structure of Echovirus 6 complexed with its uncoating rec...
+Supramolecule #1: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec...
+Macromolecule #1: Capsid protein VP1
+Macromolecule #2: Capsid protein VP2
+Macromolecule #3: Capsid protein VP3
+Macromolecule #4: Capsid protein VP4
+Macromolecule #5: IgG receptor FcRn large subunit p51
+Macromolecule #6: Beta-2-microglobulin
+Macromolecule #7: SPHINGOSINE
+Macromolecule #8: POTASSIUM ION
+Macromolecule #9: SODIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6ilm: |