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- EMDB-25905: Cryo-EM structure of W6 possum enterovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-25905
TitleCryo-EM structure of W6 possum enterovirus
Map dataEnterovirus EV-F4 - isolated from Bushtail Possum
SampleEnterovirus != Possum enterovirus W6

Enterovirus

  • Virus: Possum enterovirus W6
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: SPHINGOSINE
  • Ligand: POTASSIUM ION
  • Ligand: water
Keywordsenterovirus / icosahedral / VIRUS
Biological speciesPossum enterovirus W6
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWang I / Jayawardena N
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPAS/00011-2020 Canada
CitationJournal: Viruses / Year: 2022
Title: Cryo-EM Structure of a Possum Enterovirus.
Authors: Ivy Wang / Sandeep K Gupta / Guillaume Ems / Nadishka Jayawardena / Mike Strauss / Mihnea Bostina /
Abstract: Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess ...Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess the structural diversity of these picornaviruses. The capsid structure, determined to ~3 Å resolution by single particle analysis, exhibits a largely smooth surface, similar to EV-F3 (formerly BEV-2). Although the cellular receptor is not known, the absence of charged residues on the outer surface of the canyon suggest a different receptor type than for EV-F3. Density for the pocket factor is clear, with the entrance to the pocket being smaller than for other enteroviruses.
History
DepositionJan 12, 2022-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7thx
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7thx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25905.png

Downloads & links

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Map

FileDownload / File: emd_25905.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnterovirus EV-F4 - isolated from Bushtail Possum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 640 pix.
= 548.48 Å		0.86 Å/pix.
x 640 pix.
= 548.48 Å		0.86 Å/pix.
x 640 pix.
= 548.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.857 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126 / Movie #1: 0.0126
Minimum - Maximum-0.041131806 - 0.0651316
Average (Standard dev.)-0.0001894789 (±0.0037278403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 548.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8570.8570.857
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z548.480548.480548.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-0.0410.065-0.000

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Supplemental data

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Sample components

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Entire : Enterovirus

EntireName: Enterovirus
Components
  • Virus: Possum enterovirus W6
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: SPHINGOSINE
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Possum enterovirus W6

SupramoleculeName: Possum enterovirus W6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 263532 / Sci species name: Possum enterovirus W6 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Possum enterovirus W6

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Possum enterovirus W6
Molecular weightTheoretical: 30.311832 KDa
SequenceString: GETGQLIKDT IKNTVENTVE STHSISTEAT PALQAAETGA TSNASDESMI ETRNVVNTHG VAETSLEGFY GRAGLVAMFT TEGGIRSWY INFGKYVQLR AKLELLTYAR FDVEFTIVAQ VVDEQAKVKD FNVDYQVMYV PPGASAPDGQ DSFQWQSSCN P SVISNTGL ...String:
GETGQLIKDT IKNTVENTVE STHSISTEAT PALQAAETGA TSNASDESMI ETRNVVNTHG VAETSLEGFY GRAGLVAMFT TEGGIRSWY INFGKYVQLR AKLELLTYAR FDVEFTIVAQ VVDEQAKVKD FNVDYQVMYV PPGASAPDGQ DSFQWQSSCN P SVISNTGL PPARVSVPFM SSANAYSFSY DGYIQFGDTS SSSYGILPIH YLGQLVVRTC EDLDSARLRV RIYAKPKHMR GW IPRSPRM RPYVSRFTGI YTDAPSFCVN RESITTAG

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Possum enterovirus W6
Molecular weightTheoretical: 26.577887 KDa
SequenceString: SAEACGYSDR VAQLTLGNST ITTQEAANIV VAYGRWPSGL RDTDATAVDK PTQPGVSAER FYTLPSVQWT TSFTGHYWKL PDALSDLGL FGQNLQFHYL YRGGWAIHVQ CNATKFHQGT LLVVAVPEHK IQAQSNPSFG RTNPGEAGAA CQFPFTFEDG T ALGNALIY ...String:
SAEACGYSDR VAQLTLGNST ITTQEAANIV VAYGRWPSGL RDTDATAVDK PTQPGVSAER FYTLPSVQWT TSFTGHYWKL PDALSDLGL FGQNLQFHYL YRGGWAIHVQ CNATKFHQGT LLVVAVPEHK IQAQSNPSFG RTNPGEAGAA CQFPFTFEDG T ALGNALIY PHQWINLRTN NSATLVLPYV NAIPMDSGIK HNNWTLLVIP IVPLEYAVGA TTFVPITVTI APMCTEYNGL RA AVTQ

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Possum enterovirus W6
Molecular weightTheoretical: 26.997758 KDa
SequenceString: GCPTLYTPGS GQFLTTDDFQ TPCMLPKFQP TPVIDIPGEV KNFLEVIQVE SLVEINNVSG VEGVARYRIP LNVQDAMDGQ IMAVRVDPG ADGPMQSTLL GVFTRYYTQW SGSLDFTFMF CGTFMTTGKV IIAYTPPGGD QPGSRQQAML GTHVVWDFGL Q SSITLVVP ...String:
GCPTLYTPGS GQFLTTDDFQ TPCMLPKFQP TPVIDIPGEV KNFLEVIQVE SLVEINNVSG VEGVARYRIP LNVQDAMDGQ IMAVRVDPG ADGPMQSTLL GVFTRYYTQW SGSLDFTFMF CGTFMTTGKV IIAYTPPGGD QPGSRQQAML GTHVVWDFGL Q SSITLVVP WISSGHFRGT SLDNTIYKYR YYEAGYITMW YQTNMVVPPN FPTEASILMF VAAQPNFSLR ILKDRPDITQ VA SLQ

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Possum enterovirus W6
Molecular weightTheoretical: 7.63234 KDa
SequenceString:
MGAQLSKNTA GSHTTGTYAT GGSSIHYTNI NYYENAASNS LNKQDFTQDP DKFTRPVADI MKEAAVPLKS P

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Macromolecule #5: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 21 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.37 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1hxs


Details: filtered to 6nm
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: relion 3.1 / Number images used: 9687
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5osn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7thx:
Cryo-EM structure of W6 possum enterovirus

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