6ADS | pdb_00006ads

Structure of Seneca Valley Virus in acidic conditions

  • Classification: VIRUS
  • Organism(s): Senecavirus A
  • Mutation(s): No 

  • Deposited: 2018-08-02 Released: 2019-02-06 
  • Deposition Author(s): Lou, Z.Y., Cao, L.
  • Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1

Cao, L.Zhang, R.Liu, T.Sun, Z.Hu, M.Sun, Y.Cheng, L.Guo, Y.Fu, S.Hu, J.Li, X.Yu, C.Wang, H.Chen, H.Li, X.Fry, E.E.Stuart, D.I.Qian, P.Lou, Z.Rao, Z.

(2018) Proc Natl Acad Sci U S A 115: 13087-13092

  • DOI: https://doi.org/10.1073/pnas.1814309115
  • Primary Citation Related Structures: 
    6ADL, 6ADM, 6ADR, 6ADS, 6ADT

  • PubMed 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 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.


  • Organizational Affiliation
    • Drug Discovery Center for Infectious Disease, College of Pharmacy, Nankai University, 300071 Tianjin, China.

Macromolecule Content 

  • Total Structure Weight: 91.28 kDa 
  • Atom Count: 6,038 
  • Modeled Residue Count: 769 
  • Deposited Residue Count: 827 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP1258Senecavirus AMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VP3B [auth C]231Senecavirus AMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VP2C [auth B]267Senecavirus AMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VP471Senecavirus AMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.2: 2025-06-25
    Changes: Data collection, Structure summary