3JBC

Complex of Poliovirus with VHH PVSP29F


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site.

Strauss, M.Schotte, L.Thys, B.Filman, D.J.Hogle, J.M.

(2016) J Virol 90: 3496-3505

  • DOI: https://doi.org/10.1128/JVI.03017-15
  • Primary Citation of Related Structures:  
    3JBC, 3JBD, 3JBE, 3JBF, 3JBG

  • PubMed Abstract: 

    Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1A [auth 1]302Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2B [auth 2]272Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3C [auth 3]237Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP4D [auth 4]69Human poliovirus 1 MahoneyMutation(s): 1 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody VHH PVSP29FE [auth 7]134Camelus dromedariusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
F [auth 1]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations, Refinement description