6ADM

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP3
C
237Senecavirus AMutation(s): 0 
Find proteins for A0A1U9IRU2 (Senecavirus A)
Go to UniProtKB:  A0A1U9IRU2
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP2
B
267Senecavirus AMutation(s): 0 
Find proteins for A0A1U9IRU2 (Senecavirus A)
Go to UniProtKB:  A0A1U9IRU2
Protein Feature View
  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
258Senecavirus AMutation(s): 0 
Find proteins for A0A1U9IRU2 (Senecavirus A)
Go to UniProtKB:  A0A1U9IRU2
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
58Senecavirus AMutation(s): 0 
Find proteins for A0A1U9IRU2 (Senecavirus A)
Go to UniProtKB:  A0A1U9IRU2
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Anthrax toxin receptor 1
R
185Homo sapiensMutation(s): 1 
Gene Names: ANTXR1ATRTEM8
Find proteins for Q9H6X2 (Homo sapiens)
Go to UniProtKB:  Q9H6X2
NIH Common Fund Data Resources
PHAROS  Q9H6X2
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-01 
  • Released Date: 2019-02-06 
  • 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: 2019-02-06
    Type: Initial release