|Entry||Database: PDB / ID: 6ads|
|Title||Structure of Seneca Valley Virus in acidic conditions|
|Keywords||VIRUS / Seneca Valley virus|
|Function / homology||Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta|
Function and homology information
|Biological species||Seneca valley virus|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å|
|Authors||Lou, Z.Y. / Cao, L.|
|Funding support|| China, 1items |
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018|
Title: Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1.
Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li ...Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao /
Abstract: Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here ...Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here we determine atomic structures of mature SVV particles alone and in complex with ANTXR1 in both neutral and acidic conditions, as well as empty "spent" particles in complex with ANTXR1 in acidic conditions by cryoelectron microscopy. SVV engages ANTXR1 mainly by the VP2 DF and VP1 CD loops, leading to structural changes in the VP1 GH loop and VP3 GH loop, which attenuate interprotomer interactions and destabilize the capsid assembly. Despite lying on the edge of the attachment site, VP2 D146 interacts with the metal ion in ANTXR1 and is required for cell entry. Though the individual substitution of most interacting residues abolishes receptor binding and virus propagation, a serine-to-alanine mutation at VP2 S177 significantly increases SVV proliferation. Acidification of the SVV-ANTXR1 complex results in a major reconfiguration of the pentameric capsid assemblies, which rotate ∼20° around the icosahedral fivefold axes to form a previously uncharacterized spent particle resembling a potential uncoating intermediate with remarkable perforations at both two- and threefold axes. These structures provide high-resolution snapshots of SVV entry, highlighting opportunities for anticancer therapeutic optimization.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: VP1x 60
A: VP1x 5
A: VP1x 6
|Symmetry||Point symmetry: (Schoenflies symbol: I (icosahedral))|
|#1: Protein|| |
Mass: 28494.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
|#2: Protein|| |
Mass: 25548.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
|#3: Protein|| |
Mass: 29843.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
|#4: Protein|| |
Mass: 7393.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Seneca valley virusSenecavirus / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL|
|Source (natural)||Organism: Seneca valley virus|
|Details of virus||Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION|
|Buffer solution||pH: 6|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE-PROPANE|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Model: FEI TECNAI ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 1.63 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)|
|Software||Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13010 / Symmetry type: POINT|
|Atomic model building||Protocol: RIGID BODY FIT|
|Refine LS restraints|
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