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.USA 115: 13087-13092

  • DOI: 10.1073/pnas.1814309115
  • Primary Citation of Related Structures:  

  • 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 parti ...

    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

    Nanjing Foreign Language School, 210046 Nanjing, China.,Drug Discovery Center for Infectious Disease, College of Pharmacy, Nankai University, 300071 Tianjin, China.,Division of Structural Biology, University of Oxford, Headington, OX3 7BN Oxford, United Kingdom.,School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, 100084 Beijing, China; dave@strubi.ox.ac.uk qianp@mail.hzau.edu.cn louzy@mail.tsinghua.edu.cn.,Division of Structural Biology, University of Oxford, Headington, OX3 7BN Oxford, United Kingdom dave@strubi.ox.ac.uk qianp@mail.hzau.edu.cn louzy@mail.tsinghua.edu.cn.,College of Life Sciences, Nankai University, 300071 Tianjin, China.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China; dave@strubi.ox.ac.uk qianp@mail.hzau.edu.cn louzy@mail.tsinghua.edu.cn.,Hubei Colorectal Cancer Clinical Research Center, Hubei Cancer Hospital, 430071 Wuhan, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, 100101 Beijing, China.,Tsinghua University Affiliated High School, 100084 Beijing, China.,Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, 100084 Beijing, China.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP3
C
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP2
B
246N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Anthrax toxin receptor 1
R
185Homo sapiensMutation(s): 1 
Gene Names: ANTXR1 (ATR, TEM8)
Find proteins for Q9H6X2 (Homo sapiens)
Go to Gene View: ANTXR1
Go to UniProtKB:  Q9H6X2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
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 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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