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- PDB-6t34: Atomic model for Turnip mosaic virus (TuMV) -

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Basic information

Entry
Database: PDB / ID: 6t34
TitleAtomic model for Turnip mosaic virus (TuMV)
Components
  • Coat protein
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / potyvirus / virion / helical virus
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / RNA / Genome polyprotein / Genome polyprotein
Function and homology information
Biological speciesTurnip mosaic virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsValle, M.V. / Cuesta, R.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098996-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2015-66326-P Spain
CitationJournal: Sci Rep / Year: 2019
Title: Structure of Turnip mosaic virus and its viral-like particles.
Authors: Rebeca Cuesta / Carmen Yuste-Calvo / David Gil-Cartón / Flora Sánchez / Fernando Ponz / Mikel Valle /
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 ...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.
History
DepositionOct 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-10373
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  • EMDB-10373
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein
a: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
B: Coat protein
b: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
C: Coat protein
c: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
D: Coat protein
d: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
E: Coat protein
e: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
F: Coat protein
f: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
G: Coat protein
g: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
H: Coat protein
h: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
I: Coat protein
i: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
J: Coat protein
j: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
K: Coat protein
k: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
L: Coat protein
l: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
M: Coat protein
m: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
N: Coat protein
n: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
O: Coat protein
o: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
P: Coat protein
p: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Q: Coat protein
q: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
R: Coat protein
r: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
S: Coat protein
s: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)485,62638
Polymers485,62638
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area136340 Å2
ΔGint-684 kcal/mol
Surface area232490 Å2
MethodPISA

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Components

#1: Protein
Coat protein


Mass: 24073.395 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Source: (natural) Turnip mosaic virus (strain Japanese) / Strain: Japanese / References: UniProt: A0A1B1RVA3, UniProt: A0A346TKY7*PLUS
#2: RNA chain
RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Details: Model of ssRNA as polyU / Source: (natural) Turnip mosaic virus

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Turnip mosaic virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Turnip mosaic virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Brassica rapa subsp. rapa
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40 / Used frames/image: 3-31

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
4CTFFIND3CTF correction
7Cootmodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -40.8 ° / Axial rise/subunit: 4 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 444678
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194432 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingB value: 270 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5ODV

5odv


Pdb chain-ID: A / Accession code: 5ODV / Source name: PDB / Type: experimental model

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