3JD7

The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 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

The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs.

Lee, H.Shingler, K.L.Organtini, L.J.Ashley, R.E.Makhov, A.M.Conway, J.F.Hafenstein, S.

(2016) Sci Adv 2: e1501929-e1501929

  • DOI: 10.1126/sciadv.1501929

  • PubMed Abstract: 
  • Many nonenveloped viruses engage host receptors that initiate capsid conformational changes necessary for genome release. Structural studies on the mechanisms of picornavirus entry have relied on in vitro approaches of virus incubated at high tempera ...

    Many nonenveloped viruses engage host receptors that initiate capsid conformational changes necessary for genome release. Structural studies on the mechanisms of picornavirus entry have relied on in vitro approaches of virus incubated at high temperatures or with excess receptor molecules to trigger the entry intermediate or A-particle. We have induced the coxsackievirus B3 entry intermediate by triggering the virus with full-length receptors embedded in lipid bilayer nanodiscs. These asymmetrically formed A-particles were reconstructed using cryo-electron microscopy and a direct electron detector. These first high-resolution structures of a picornavirus entry intermediate captured at a membrane with and without imposing icosahedral symmetry (3.9 and 7.8 Å, respectively) revealed a novel A-particle that is markedly different from the classical A-particles. The asymmetric receptor binding triggers minimal global capsid expansion but marked local conformational changes at the site of receptor interaction. In addition, viral proteins extrude from the capsid only at the site of extensive protein remodeling adjacent to the nanodisc. Thus, the binding of the receptor triggers formation of a unique site in preparation for genome release.


    Organizational Affiliation

    The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
1
281Coxsackievirus B3Mutation(s): 0 
Find proteins for Q5UEA3 (Coxsackievirus B3)
Go to UniProtKB:  Q5UEA3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
2
263Coxsackievirus B3Mutation(s): 0 
Find proteins for Q5UEA3 (Coxsackievirus B3)
Go to UniProtKB:  Q5UEA3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
3
238Coxsackievirus B3Mutation(s): 0 
Find proteins for Q5UEA3 (Coxsackievirus B3)
Go to UniProtKB:  Q5UEA3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4
4
68Coxsackievirus B3Mutation(s): 0 
Find proteins for Q5UEA3 (Coxsackievirus B3)
Go to UniProtKB:  Q5UEA3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download SDF File 
Download CCD File 
1
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release