8ACC

CryoEM structure of sweet potato mild mottle virus VLP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CryoEM and stability analysis of virus-like particles of potyvirus and ipomovirus infecting a common host.

Chase, O.Javed, A.Byrne, M.J.Thuenemann, E.C.Lomonossoff, G.P.Ranson, N.A.Lopez-Moya, J.J.

(2023) Commun Biol 6: 433-433

  • DOI: https://doi.org/10.1038/s42003-023-04799-x
  • Primary Citation of Related Structures:  
    8ACB, 8ACC

  • PubMed Abstract: 

    Sweet potato feathery mottle virus (SPFMV) and Sweet potato mild mottle virus (SPMMV) are members of the genera Potyvirus and Ipomovirus, family Potyviridae, sharing Ipomoea batatas as common host, but transmitted, respectively, by aphids and whiteflies. Virions of family members consist of flexuous rods with multiple copies of a single coat protein (CP) surrounding the RNA genome. Here we report the generation of virus-like particles (VLPs) by transient expression of the CPs of SPFMV and SPMMV in the presence of a replicating RNA in Nicotiana benthamiana. Analysis of the purified VLPs by cryo-electron microscopy, gave structures with resolutions of 2.6 and 3.0 Å, respectively, showing a similar left-handed helical arrangement of 8.8 CP subunits per turn with the C-terminus at the inner surface and a binding pocket for the encapsidated ssRNA. Despite their similar architecture, thermal stability studies reveal that SPMMV VLPs are more stable than those of SPFMV.


  • Organizational Affiliation

    Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193, Cerdanyola del Vallès, Barcelona, Spain.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein302Sweet potato mild mottle virusMutation(s): 0 
UniProt
Find proteins for Q599X9 (Sweet potato mild mottle virus)
Explore Q599X9 
Go to UniProtKB:  Q599X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ599X9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Single-stranded RNA5Nicotiana tabacum
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019-105692RB-100
Ministerio de Ciencia e Innovacion (MCIN)SpainCEX2019-000902-S
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R001669/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T004703/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Source and taxonomy