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- EMDB-30375: Cryo-EM Structure of Apple Latent Spherical Virus (ALSV) -

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Basic information

Entry
Database: EMDB / ID: EMD-30375
TitleCryo-EM Structure of Apple Latent Spherical Virus (ALSV)
Map data
Sample
  • Virus: Apple latent spherical virus
    • Protein or peptide: VP20 protein
    • Protein or peptide: VP24 protein
    • Protein or peptide: VP25 protein
KeywordsCheravirus / capsid stabilization / genome release / single particle cryo-EM / STRUCTURAL PROTEIN
Function / homology: / : / : / Capsid protein Vp25 / Capsid protein Vp20 / Capsid protein Vp24 / virion component / Viral coat protein subunit / 108K polyprotein
Function and homology information
Biological speciesApple latent spherical virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsNaitow H / Hamaguchi T
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H04757 Japan
Japan Society for the Promotion of Science (JSPS)24657111 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Commun Biol / Year: 2020
Title: Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release.
Authors: Hisashi Naitow / Tasuku Hamaguchi / Saori Maki-Yonekura / Masamichi Isogai / Nobuyuki Yoshikawa / Koji Yonekura /
Abstract: Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet ...Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle cryo-electron microscopy (cryo-EM) with a cold-field emission beam. The cryo-EM map reveals a unique structure composed of three capsid proteins Vp25, Vp20, and Vp24. Strikingly Vp25 has a long N-terminal extension, which substantially stabilises the capsid frame of Vp25 and Vp20 subunits. Cryo-EM images also resolve RNA genome leaking from a pentameric protrusion of Vp24 subunits. The structures and observations suggest that genome release occurs through occasional opening of the Vp24 subunits, possibly suppressed to a low frequency by the rigid frame of the other subunits.
History
DepositionJul 6, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7chk
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7chk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30375.png

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Map

FileDownload / File: emd_30375.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 512 pix.
= 634.88 Å		1.24 Å/pix.
x 512 pix.
= 634.88 Å		1.24 Å/pix.
x 512 pix.
= 634.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0394385 - 0.08309689
Average (Standard dev.)-0.0000310393 (±0.0038638904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 634.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z634.880634.880634.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0390.083-0.000

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Supplemental data

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Sample components

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Entire : Apple latent spherical virus

EntireName: Apple latent spherical virus
Components
  • Virus: Apple latent spherical virus
    • Protein or peptide: VP20 protein
    • Protein or peptide: VP24 protein
    • Protein or peptide: VP25 protein

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Supramolecule #1: Apple latent spherical virus

SupramoleculeName: Apple latent spherical virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: ALSV was purified and isolated from infected Chenopodium quinoa leaf.
NCBI-ID: 101688 / Sci species name: Apple latent spherical virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Malus domestica (apple)
Virus shellShell ID: 1 / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: VP20 protein

MacromoleculeName: VP20 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Apple latent spherical virus
Molecular weightTheoretical: 19.957994 KDa
SequenceString:
GACLSIPNFP VHITGKTQQL HVGPKPSIAR FSFNPFDLGT VFNRFQSLCA HLEGYSGDLI VNWLVTCSAL TNARLYIIPV YDNYSFEKF SEEKLIQCKY EFKQISLVRK GTVHIPFVNW FGSYSRTRFP KLLFYFPNGV SGPSGEKIHV TVQLDRILNF S GLGHRLFK EIGPLVGE

UniProtKB: 108K polyprotein

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Macromolecule #2: VP24 protein

MacromoleculeName: VP24 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Apple latent spherical virus
Molecular weightTheoretical: 21.575467 KDa
SequenceString: GSDPFSFLLN YSHCGTLVES SLNKGGMWCV PVSPVNLAAY TLQGEALVFN DAFVSKTHNW LHFMASTTAY WRGTLHYQMR VTYKDRNAA CRNLVAFYTT NNESLFGFNN KPVGDTGISS VMGDSFSVDI TVPFLIPTCY LQTIRGKFDY LNSCNGCIYF H LPTKSATS ...String:
GSDPFSFLLN YSHCGTLVES SLNKGGMWCV PVSPVNLAAY TLQGEALVFN DAFVSKTHNW LHFMASTTAY WRGTLHYQMR VTYKDRNAA CRNLVAFYTT NNESLFGFNN KPVGDTGISS VMGDSFSVDI TVPFLIPTCY LQTIRGKFDY LNSCNGCIYF H LPTKSATS VQLWVRPGQD FDFARFRLLK AGYT

UniProtKB: 108K polyprotein

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Macromolecule #3: VP25 protein

MacromoleculeName: VP25 protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Apple latent spherical virus
Molecular weightTheoretical: 24.098459 KDa
SequenceString: GPDFTKIIWP TVVERNFSNP QSEITTTLQE LYGDTFETVS ICPPQSYGGE LLKGKIFFSS TPEFTREDLV EGKILASFKL DEVLSGLGM GAMLMTQIMS GHATIRVSAK VMLSKFCSFA LKLVYDELMQ LNSDTTDFGK ISVLPGAIFS TQEEEFSFDF E LFSPGVHL ...String:
GPDFTKIIWP TVVERNFSNP QSEITTTLQE LYGDTFETVS ICPPQSYGGE LLKGKIFFSS TPEFTREDLV EGKILASFKL DEVLSGLGM GAMLMTQIMS GHATIRVSAK VMLSKFCSFA LKLVYDELMQ LNSDTTDFGK ISVLPGAIFS TQEEEFSFDF E LFSPGVHL KFDNNKLLGK VHLAALSAPN LTENMPESFS CTFNFSIVDV KTTFYNIGQ

UniProtKB: 108K polyprotein

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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 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormula
0.1 MTris-HCl
0.1 MNaCl
5.0 mMMgCl
Sugar embeddingMaterial: ice
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
DetailsIn practice, the sample concentration is 1-2 mg/ml.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 8.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8018
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7chk:
Cryo-EM Structure of Apple Latent Spherical Virus (ALSV)

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