3JBD

Complex of poliovirus with VHH PVSP6A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1128/JVI.03017-15
  • Primary Citation of Related Structures:  

  • 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-electr ...

    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.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA james_hogle@hms.harvard.edu.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pharmaceutical Biotechnology and Molecular Biology, Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Pharmaceutical Biotechnology and Molecular Biology, Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium Department of Clinical Chemistry and Radio-immunology, Universitair Ziekenhuis Brussel, Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
1
302Poliovirus type 1 (strain Mahoney)Mutation(s): 0 
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Go to UniProtKB:  P03300
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
2
272Poliovirus type 1 (strain Mahoney)Mutation(s): 0 
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Go to UniProtKB:  P03300
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
3
237Poliovirus type 1 (strain Mahoney)Mutation(s): 0 
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Go to UniProtKB:  P03300
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4
4
69Poliovirus type 1 (strain Mahoney)Mutation(s): 0 
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Go to UniProtKB:  P03300
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
nanobody VHH PVSP6A
7
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MYR
Query on MYR
4
NON-POLYMERC14 H28 O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 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: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection