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- EMDB-1688: CryoEM reconstruction of human parechovirus 1 complexed with inte... -

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Basic information

Entry
Database: EMDB / ID: EMD-1688
TitleCryoEM reconstruction of human parechovirus 1 complexed with integrin alphaV-beta3
Map dataThis is a cryoEM reconstruction of human parechovirus 1 complexed with integrin alphaV-beta3 at 15 angstrom resolution
Sample
  • Sample: Purified human parechovirus 1 in 1 mM MgCl2 and integrin alphaV-beta6 in PBS buffer
  • Virus: Human parechovirus 1
  • Protein or peptide: Integrin alphaV-beta3
Keywordspicornavirus / parechovirus / icosahedral / integrin
Biological speciesHomo sapiens (human) / Human parechovirus 1
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.0 Å
AuthorsSeitsonen JJT / Susi P / Heikkila O / Laurinmaki P / Hyypia T / Butcher SJ
CitationJournal: J Virol / Year: 2010
Title: Interaction of alphaVbeta3 and alphaVbeta6 integrins with human parechovirus 1.
Authors: Jani Seitsonen / Petri Susi / Outi Heikkilä / Robert S Sinkovits / Pasi Laurinmäki / Timo Hyypiä / Sarah J Butcher /
Abstract: Human parechovirus (HPEV) infections are very common in early childhood and can be severe in neonates. It has been shown that integrins are important for cellular infectivity of HPEV1 through ...Human parechovirus (HPEV) infections are very common in early childhood and can be severe in neonates. It has been shown that integrins are important for cellular infectivity of HPEV1 through experiments using peptide blocking assays and function-blocking antibodies to alpha(V) integrins. The interaction of HPEV1 with alpha(V) integrins is presumably mediated by a C-terminal RGD motif in the capsid protein VP1. We characterized the binding of integrins alpha(V)beta(3) and alpha(V)beta(6) to HPEV1 by biochemical and structural studies. We showed that although HPEV1 bound efficiently to immobilized integrins, alpha(V)beta(6) bound more efficiently than alpha(V)beta(3) to immobilized HPEV1. Moreover, soluble alpha(V)beta(6), but not alpha(V)beta(3), blocked HPEV1 cellular infectivity, indicating that it is a high-affinity receptor for HPEV1. We also showed that HPEV1 binding to integrins in vitro could be partially blocked by RGD peptides. Using electron cryo-microscopy and image reconstruction, we showed that HPEV1 has the typical T=1 (pseudo T=3) organization of a picornavirus. Complexes of HPEV1 and integrins indicated that both integrin footprints reside between the 5-fold and 3-fold symmetry axes. This result does not match the RGD position predicted from the coxsackievirus A9 X-ray structure but is consistent with the predicted location of this motif in the shorter C terminus found in HPEV1. This first structural characterization of a parechovirus indicates that the differences in receptor binding are due to the amino acid differences in the integrins rather than to significantly different viral footprints.
History
DepositionJan 25, 2010-
Header (metadata) releaseSep 17, 2010-
Map releaseSep 17, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1688_HPE...

Downloads & links

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Map

FileDownload / File: emd_1688.map.gz / Format: CCP4 / Size: 120.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis is a cryoEM reconstruction of human parechovirus 1 complexed with integrin alphaV-beta3 at 15 angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 401 pix.
= 453.13 Å		1.13 Å/pix.
x 401 pix.
= 453.13 Å		1.13 Å/pix.
x 401 pix.
= 453.13 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-625.0 - 2005.0
Average (Standard dev.)0.1685688 (±499.720611570000017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions401401401
Spacing401401401
CellA=B=C: 453.13 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.131.131.13
M x/y/z401401401
origin x/y/z0.0000.0000.000
length x/y/z453.130453.130453.130
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS401401401
D min/max/mean-625.0002005.0000.169

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Supplemental data

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Sample components

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Entire : Purified human parechovirus 1 in 1 mM MgCl2 and integrin alphaV-b...

EntireName: Purified human parechovirus 1 in 1 mM MgCl2 and integrin alphaV-beta6 in PBS buffer
Components
  • Sample: Purified human parechovirus 1 in 1 mM MgCl2 and integrin alphaV-beta6 in PBS buffer
  • Virus: Human parechovirus 1
  • Protein or peptide: Integrin alphaV-beta3

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Supramolecule #1000: Purified human parechovirus 1 in 1 mM MgCl2 and integrin alphaV-b...

SupramoleculeName: Purified human parechovirus 1 in 1 mM MgCl2 and integrin alphaV-beta6 in PBS buffer
type: sample / ID: 1000
Oligomeric state: Complete particle (60-mer) with the RNA genome inside with few integrin molecules attached
Number unique components: 2

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Supramolecule #1: Human parechovirus 1

SupramoleculeName: Human parechovirus 1 / type: virus / ID: 1 / Name.synonym: HPEV1 / NCBI-ID: 12063 / Sci species name: Human parechovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HPEV1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 5.1 MDa
Virus shellShell ID: 1 / Name: native / Diameter: 280 Å / T number (triangulation number): 1

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Macromolecule #1: Integrin alphaV-beta3

MacromoleculeName: Integrin alphaV-beta3 / type: protein_or_peptide / ID: 1 / Name.synonym: Integrin alphaV-beta3 / Details: Product of BioMarket Ltd., Finland / Number of copies: 1 / Oligomeric state: Heterodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightTheoretical: 203 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.24 mg/mL
BufferpH: 7.2 / Details: 1 mM MgCl2 in PBS
StainingType: NEGATIVE / Details: Cryo preparation
GridDetails: 400 mesh carbon coated copper
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Guillotine / Method: Blot for 1-2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.922 µm / Nominal defocus min: 1.486 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 91 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 62,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 16 / Average electron dose: 18 e/Å2 / Details: Scanned with Zeiss Photoscan TD scanner
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 431

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