5APM image
Deposition Date 2015-09-17
Release Date 2016-07-27
Last Version Date 2024-05-08
Entry Detail
PDB ID:
5APM
Keywords:
Title:
Multiple capsid-stabilizing protein-RNA and protein-protein interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
4.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:VP1
Chain IDs:A
Chain Length:198
Number of Molecules:1
Biological Source:HUMAN PARECHOVIRUS 3
Polymer Type:polypeptide(L)
Molecule:VP3
Chain IDs:B
Chain Length:237
Number of Molecules:1
Biological Source:HUMAN PARECHOVIRUS 3
Polymer Type:polypeptide(L)
Molecule:VP0
Chain IDs:C
Chain Length:263
Number of Molecules:1
Biological Source:HUMAN PARECHOVIRUS 3
Primary Citation
Multiple Capsid-Stabilizing Interactions Revealed in a High-Resolution Structure of an Emerging Picornavirus Causing Neonatal Sepsis
Nat.Commun. 7 11387 ? (2016)
PMID: 27435188 DOI: 10.1038/NCOMMS11387

Abstact

The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.

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Primary Citation of related structures