6ADL

Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley Virus in acidic conditions

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 10.1073/pnas.1814309115
  • Primary Citation of 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 ...

    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: 

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, 100101 Beijing, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP1A230Senecavirus AMutation(s): 0 
UniProt
Find proteins for A0A1I9WAH6 (Senecavirus A)
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Go to UniProtKB:  A0A1I9WAH6
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UniProt GroupA0A1I9WAH6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VP3B [auth C]238Senecavirus AMutation(s): 0 
UniProt
Find proteins for A0A1I9WAH6 (Senecavirus A)
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Go to UniProtKB:  A0A1I9WAH6
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UniProt GroupA0A1I9WAH6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VP2C [auth B]246Senecavirus AMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.19.12 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002))
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UniProt GroupQ155Z9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Anthrax toxin receptor 1D [auth R]185Homo sapiensMutation(s): 1 
Gene Names: ANTXR1, ATR, TEM8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6X2 (Homo sapiens)
Explore Q9H6X2 
Go to UniProtKB:  Q9H6X2
PHAROS:  Q9H6X2
GTEx:  ENSG00000169604 
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UniProt GroupQ9H6X2
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
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E [auth R]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-01 
  • Released Date: 2019-12-25 
    • Deposition Author(s): Lou, Z.Y., Cao, L.
Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release