6T34 | pdb_00006t34

Atomic model for Turnip mosaic virus (TuMV)

  • Classification: VIRUS
  • Organism(s): Turnip mosaic virus
  • Mutation(s): No 

  • Deposited: 2019-10-10 Released: 2019-11-13 
  • Deposition Author(s): Valle, M.V., Cuesta, R.
  • Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Structure of Turnip mosaic virus and its viral-like particles.

Cuesta, R., Yuste-Calvo, C., Gil-Carton, D., Sanchez, F., Ponz, F., Valle, M.

(2019) Sci Rep 9: 15396-15396

  • DOI: https://doi.org/10.1038/s41598-019-51823-4
  • Primary Citation Related Structures: 
    6T34

  • PubMed Abstract: 

    Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion.

    • Organizational Affiliation: 
    • Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain.

Macromolecule Content 

  • Total Structure Weight: 485.63 kDa 
  • Atom Count: 33,915 
  • Modeled Residue Count: 4,028 
  • Deposited Residue Count: 4,028 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coat protein207Turnip mosaic virusMutation(s): 0 
UniProt
Find proteins for A0A346TKY7 (Turnip mosaic virus (strain Japanese))
Explore A0A346TKY7 
Go to UniProtKB:  A0A346TKY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A346TKY7
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*U)-3')5Turnip mosaic virus
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2
MODEL REFINEMENTPHENIX

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPGC2018-098996-B-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2015-66326-P

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection, Database references, Refinement description