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- PDB-6ilj: Cryo-EM structure of Echovirus 6 complexed with its attachment re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ilj | ||||||
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Title | Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 | ||||||
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![]() | VIRUS / Echovirus 6 / CD55 / Cryo-EM / virus-receptor complex | ||||||
Function / homology | ![]() regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Gao, G.F. / Liu, S. / Zhao, X. / Peng, R. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.1 KB | Display | ![]() |
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PDB format | ![]() | 155.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 876.8 KB | Display | ![]() |
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Full document | ![]() | 881.4 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 60.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9684MC ![]() 9685C ![]() 9686C ![]() 9687C ![]() 9688C ![]() 9689C ![]() 9690C ![]() 6ilkC ![]() 6illC ![]() 6ilmC ![]() 6ilnC ![]() 6iloC ![]() 6ilpC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
-Capsid protein ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 31707.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 28064.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 26378.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 7338.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein / Non-polymers , 2 types, 2 molecules E![](data/chem/img/SPH.gif)
![](data/chem/img/SPH.gif)
#5: Protein | Mass: 21307.959 Da / Num. of mol.: 1 / Fragment: UNP residues 94-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#6: Chemical | ChemComp-SPH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: ![]() |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 5.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11494 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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