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- EMDB-6147: Cryo-EM reconstruction of poliovirus-receptor complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6147
TitleCryo-EM reconstruction of poliovirus-receptor complex
Map dataReconstruction of poliovirus-receptor complex using deglycosylated receptor
Sample
  • Sample: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
  • Virus: Human poliovirus 1 Mahoney
  • Protein or peptide: Poliovirus receptor
Keywordspoliovirus / receptor / PVR / CD155
Function / homology
Function and homology information


susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / symbiont-mediated suppression of host translation initiation / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / symbiont-mediated suppression of host translation initiation / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / adherens junction / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nucleoside-triphosphate phosphatase / channel activity / signaling receptor activity / virus receptor activity / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Immunoglobulin V-Type / Picornavirus/Calicivirus coat protein / Immunoglobulin V-set domain / Viral coat protein subunit / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Poliovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Human poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsStrauss M / Filman DJ / Cheng N / Noel RT / Belnap DM / 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
DepositionOct 15, 2014-
Header (metadata) releaseNov 26, 2014-
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: 0.00688
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00688
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j8f
  • Surface level: 0.00688
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j8f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6147.gif

Downloads & links

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Map

FileDownload / File: emd_6147.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of poliovirus-receptor complex using deglycosylated receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 640 pix.
= 631.04 Å		0.99 Å/pix.
x 640 pix.
= 631.04 Å		0.99 Å/pix.
x 640 pix.
= 631.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.986 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00688 / Movie #1: 0.00688
Minimum - Maximum-0.01532988 - 0.04193989
Average (Standard dev.)-0.00157756 (±0.005511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-319-319-319
Dimensions640640640
Spacing640640640
CellA=B=C: 631.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9860.9860.986
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z631.040631.040631.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-319-319-319
NC/NR/NS640640640
D min/max/mean-0.0150.042-0.002

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Supplemental data

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Sample components

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Entire : Type I poliovirus (Mahoney) in complex with enzymatically deglyco...

EntireName: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
Components
  • Sample: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
  • Virus: Human poliovirus 1 Mahoney
  • Protein or peptide: Poliovirus receptor

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Supramolecule #1000: Type I poliovirus (Mahoney) in complex with enzymatically deglyco...

SupramoleculeName: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
type: sample / ID: 1000 / Oligomeric state: 1 icosahedral virus + 60 receptors / Number unique components: 2
Molecular weightTheoretical: 12 MDa

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 9 MDa
Virus shellShell ID: 1 / Diameter: 165 Å / 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/CD155, Nectin-like protein 5, NECL-5 / Number of copies: 60 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Poliovirus receptor

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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

Concentration1.0 mg/mL
BufferpH: 7 / Details: PBS
GridDetails: 200 mesh Cu grid with fenestrated carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 45 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Method: Sample mixed and frozen within 2 minutes.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 165 K / Average: 100 K
Alignment procedureLegacy - Electron beam tilt params: 0
DetailsK2 Summit super-resolution mode used
DateNov 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 2.5 µm / Number real images: 285 / Average electron dose: 25 e/Å2 / Details: The last 23 frames of a 24-frame stack were used. / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 25355 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 27500
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: per micrograph
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: Relion1.2, GeFrealign / Number images used: 9248

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Atomic model buiding 1

Initial modelPDB ID:

1hxs


Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 2 / Chain - #2 - Chain ID: 3 / Chain - #3 - Chain ID: 4
SoftwareName: Coot, spdbv, Refmac5
DetailsAfter rigid-body fitting, manual rebuilding of the model was alternated with automated stereochemically restrained refinement, minimizing the discrepancy between the experimental and model-based Fourier amplitudes and phases.
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: pseudo-real space
Output model

PDB-3j8f:
Cryo-EM reconstruction of poliovirus-receptor complex

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