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- EMDB-6242: Poliovirus complexed with soluble, glycosylated poliovirus recept... -

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Basic information

Entry
Database: EMDB / ID: EMD-6242
TitlePoliovirus complexed with soluble, glycosylated poliovirus receptor (Pvr) at 4 degrees C
Map data3D reconstruction of poliovirus-receptor complex
Sample
  • Sample: Poliovirus type 1 (Mahoney strain) bound to soluble, glycosylated poliovirus receptor (Pvr)
  • Virus: Human poliovirus 1
  • Protein or peptide: Poliovirus receptorCD155
Keywordscell entry / enterovirus / glycosylation / icosahedral virus / icosahedron / picornavirus / virus entry / virus-receptor complex / virus-receptor interaction
Biological speciesHomo sapiens (human) / Human poliovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsStrauss M / Filman DJ / Belnap DM / Cheng N / Noel RT / Hogle JM
CitationJournal: J Virol / Year: 2015
Title: Nectin-like interactions between poliovirus and its receptor trigger conformational changes associated with cell entry.
Authors: Mike Strauss / David J Filman / David M Belnap / Naiqian Cheng / Roane T Noel / James M Hogle /
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 ...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.
IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into ...IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into three-dimensional experimental maps of the receptor-virus complex. The molecular interactions we see between poliovirus and its receptor are reminiscent of the nectin family, by involving the burying of otherwise-exposed hydrophobic groups. Importantly, poliovirus expansion is regulated by the binding of a lipid molecule within the viral capsid. We show that receptor binding either causes this molecule to be expelled or requires it, but that its loss is not sufficient to trigger irreversible expansion. Based on our model, we propose testable hypotheses to explain how the viral shell becomes destabilized, leading to RNA uncoating. These findings give us a better understanding of how poliovirus has evolved to exploit a natural process of its host to penetrate the membrane barrier.
History
DepositionJan 14, 2015-
Header (metadata) releaseFeb 4, 2015-
Map releaseFeb 4, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 53
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6242.map.gz / Format: CCP4 / Size: 88.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of poliovirus-receptor complex
Voxel sizeX=Y=Z: 1.7947 Å
Density
Contour LevelBy AUTHOR: 53.0 / Movie #1: 53
Minimum - Maximum-105.672157290000001 - 257.799713129999986
Average (Standard dev.)11.37724972 (±47.543106080000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-143-143-143
Dimensions287287287
Spacing287287287
CellA=B=C: 515.0789 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.79470034843211.79470034843211.7947003484321
M x/y/z287287287
origin x/y/z0.0000.0000.000
length x/y/z515.079515.079515.079
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS-143-143-143
NC/NR/NS287287287
D min/max/mean-105.672257.80011.377

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Supplemental data

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Sample components

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Entire : Poliovirus type 1 (Mahoney strain) bound to soluble, glycosylated...

EntireName: Poliovirus type 1 (Mahoney strain) bound to soluble, glycosylated poliovirus receptor (Pvr)
Components
  • Sample: Poliovirus type 1 (Mahoney strain) bound to soluble, glycosylated poliovirus receptor (Pvr)
  • Virus: Human poliovirus 1
  • Protein or peptide: Poliovirus receptorCD155

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Supramolecule #1000: Poliovirus type 1 (Mahoney strain) bound to soluble, glycosylated...

SupramoleculeName: Poliovirus type 1 (Mahoney strain) bound to soluble, glycosylated poliovirus receptor (Pvr)
type: sample / ID: 1000 / Oligomeric state: 60 Pvr bind to one poliovirus / Number unique components: 2

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Supramolecule #1: Human poliovirus 1

SupramoleculeName: Human poliovirus 1 / type: virus / ID: 1 / Name.synonym: poliovirus / NCBI-ID: 12080 / Sci species name: Human poliovirus 1 / Sci species strain: Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: poliovirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Poliovirus receptor

MacromoleculeName: Poliovirus receptor / type: protein_or_peptide / ID: 1 / Name.synonym: Pvr, Nectin-like protein 5 / Number of copies: 60 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateNov 1, 1999
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Number images used: 4808

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Atomic model buiding 1

Initial modelPDB ID:
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT

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