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Open data
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Basic information
Entry | Database: PDB / ID: 7dpg | ||||||
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Title | Cryo-EM structure of Coxsackievirus B1 empty particle | ||||||
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Function / homology | ![]() symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, S. / Zhu, R. / Xu, L. / Cheng, T. / Zheng, Q. / Xia, N. | ||||||
![]() | ![]() Title: Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating. Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing ...Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing Zhang / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Lisheng Yang / Che Liu / Yuqiong Que / Mujin Fang / Ying Gu / Jun Zhang / Wenxin Luo / Z Hong Zhou / Shaowei Li / Tong Cheng / Ningshao Xia / ![]() ![]() Abstract: Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a ...Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a hydrophobic pocket formed by the major viral capsid protein, VP1. Coxsackievirus and adenovirus receptor (CAR) is a universal uncoating receptor of group B coxsackieviruses (CVB). Here, we present five high-resolution cryoEM structures of CVB representing different stages of virus infection. Structural comparisons show that the CAR penetrates deeper into the canyon than other uncoating receptors, leading to a cascade of events: collapse of the VP1 hydrophobic pocket, high-efficiency release of the pocket factor and viral uncoating and genome release under neutral pH, as compared with low pH. Furthermore, we identified a potent therapeutic antibody that can neutralize viral infection by interfering with virion-CAR interactions, destabilizing the capsid and inducing virion disruption. Together, these results define the structural basis of CVB cell entry and antibody neutralization. | ||||||
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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 | ![]() | 132.2 KB | Display | ![]() |
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PDB format | ![]() | 101.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30806MC ![]() 7dpfC ![]() 7dpzC ![]() 7dq1C ![]() 7dq4C ![]() 7dq7C 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
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Symmetry | Point symmetry: (Schoenflies symbol![]() ![]() |
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Components
#1: Protein | ![]() Mass: 31207.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 29122.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 26328.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Coxsackievirus B1 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3259: / Classification: refinement |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction![]() | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25320 / Symmetry type: POINT |