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

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Basic information

Entry
Database: PDB / ID: 7chk
TitleCryo-EM Structure of Apple Latent Spherical Virus (ALSV)
Components
  • VP20 protein
  • VP24 protein
  • VP25 protein
KeywordsSTRUCTURAL PROTEIN / Cheravirus / capsid stabilization / genome release / single particle cryo-EM
Function / homologyViral coat protein subunit / 108K polyprotein
Function and homology information
Biological speciesApple latent spherical virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsNaitow, H. / Hamaguchi, T. / Maki-Yonekura, S. / Isogai, M. / Yoshikawa, N. / Yonekura, K.
Funding support Japan, 3items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-30375
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  • Superimposition on EM map
  • EMDB-30375
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP20 protein
B: VP24 protein
C: VP25 protein


Theoretical massNumber of molelcules
Total (without water)65,6323
Polymers65,6323
Non-polymers00
Water00
1
A: VP20 protein
B: VP24 protein
C: VP25 protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,937,915180
Polymers3,937,915180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP20 protein
B: VP24 protein
C: VP25 protein
x 5


  • icosahedral pentamer
  • 328 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)328,16015
Polymers328,16015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP20 protein
B: VP24 protein
C: VP25 protein
x 6


  • icosahedral 23 hexamer
  • 394 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)393,79218
Polymers393,79218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP20 protein


Mass: 19957.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Apple latent spherical virus / References: UniProt: Q9JGP1
#2: Protein VP24 protein


Mass: 21575.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Apple latent spherical virus / References: UniProt: Q9JGP1
#3: Protein VP25 protein


Mass: 24098.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Apple latent spherical virus / References: UniProt: Q9JGP1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Apple latent spherical virus / Type: VIRUS
Details: ALSV was purified and isolated from infected Chenopodium quinoa leaf.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Apple latent spherical virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Malus domestica
Virus shellDiameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.8
Buffer component
IDConc.FormulaBuffer-ID
10.1 MTris-HCl1
20.1 MNaCl1
35 mMMgCl1
SpecimenConc.: 1 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: In practice, the sample concentration is 1-2 mg/ml.
Specimen supportGrid material: COPPER / Grid type: Quantifoil
EM embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL
Image recordingElectron dose: 8.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8018 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 52.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0074309
ELECTRON MICROSCOPYf_angle_d0.64655838
ELECTRON MICROSCOPYf_chiral_restr0.0471650
ELECTRON MICROSCOPYf_plane_restr0.0046734
ELECTRON MICROSCOPYf_dihedral_angle_d2.93932520

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