3J9F

Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Nectin-Like Interactions between Poliovirus and Its Receptor Trigger Conformational Changes Associated with Cell Entry.

Strauss, M.Filman, D.J.Belnap, D.M.Cheng, N.Noel, R.T.Hogle, J.M.

(2015) J Virol 89: 4143-4157

  • DOI: https://doi.org/10.1128/JVI.03101-14
  • Primary Citation of Related Structures:  
    3J8F, 3J9F

  • PubMed Abstract: 

    Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to form an expanded form of the capsid called the 135S particle. This expansion results in the externalization of the myristoylated capsid protein VP4 and the N-terminal extension of the capsid protein VP1, both of which become inserted into the cell membrane. Structures of the expanded forms of poliovirus and of several related viruses have recently been reported. However, until now, it has been unclear how receptor binding triggers viral expansion at physiological temperature. Here, we report poliovirus in complex with an enzymatically partially deglycosylated form of the 3-domain ectodomain of Pvr at a 4-Å resolution, as determined by cryo-electron microscopy. The interaction of the receptor with the virus in this structure is reminiscent of the interactions of Pvr with its natural ligands. At a low temperature, the receptor induces very few changes in the structure of the virus, with the largest changes occurring within the footprint of the receptor, and in a loop of the internal protein VP4. Changes in the vicinity of the receptor include the displacement of a natural lipid ligand (called "pocket factor"), demonstrating that the loss of this ligand, alone, is not sufficient to induce particle expansion. Finally, analogies with naturally occurring ligand binding in the nectin family suggest which specific structural rearrangements in the virus-receptor complex could help to trigger the irreversible expansion of the capsid.


  • 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
Protein VP1A [auth 1]302Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
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Go to UniProtKB:  P03300
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UniProt GroupP03300
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP2B [auth 2]272Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
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UniProt GroupP03300
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP3C [auth 3]238Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
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UniProt GroupP03300
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP4D [auth 4]69Human poliovirus 1 MahoneyMutation(s): 1 
UniProt
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UniProt GroupP03300
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptorE [auth 7]116Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P15151 (Homo sapiens)
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PHAROS:  P15151
GTEx:  ENSG00000073008 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptorF [auth 8]102Homo sapiensMutation(s): 0 
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PHAROS:  P15151
GTEx:  ENSG00000073008 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptorG [auth 9]92Homo sapiensMutation(s): 0 
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Find proteins for P15151 (Homo sapiens)
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PHAROS:  P15151
GTEx:  ENSG00000073008 
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Oligosaccharides

Help

Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth A],
L [auth E]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth B]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF
GlyCosmos:  G42466VF
GlyGen:  G42466VF
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth C],
K [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth F]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
N [auth 1]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
O [auth 9]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2022-12-21
    Changes: Database references, Derived calculations, Refinement description, Structure summary