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- PDB-6rtk: CryoEM structure of modified Turnip Yellows Virus devoid of minor... -

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Basic information

Entry
Database: PDB / ID: 6rtk
TitleCryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain
ComponentsMajor capsid protein
KeywordsVIRUS
Function / homologyLuteovirus group 1 coat protein / Luteovirus coat protein / T=3 icosahedral viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesTurnip yellows virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsTrapani, S. / Lai Kee Him, J. / Hoh, F. / Brault, V. / Bron, P.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05 France
CitationJournal: To Be Published
Title: CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain
Authors: Trapani, S. / Lai Kee Him, J. / Boissinot, S. / Reinbold, C. / Fallet, C. / Ancelin, A. / Lecorre, F. / Hoh, F. / Ziegler-Graff, V. / Brault, V. / Bron, P.
History
DepositionMay 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 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

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Structure visualization

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)67,5683
Polymers67,5683
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)4,054,054180
Polymers4,054,054180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodPISA

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Components

#1: Protein Major capsid protein / Coat protein / CP


Mass: 22522.520 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Turnip yellows virus (isolate FL-1) / Strain: isolate FL-1 / References: UniProt: P09508

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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: Beet western yellows virus-FL1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Beet western yellows virus-FL1
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Virus shellName: capsid / Triangulation number (T number): 3
Buffer solutionpH: 6
Buffer componentConc.: 0.1 mol / L / Name: citrate
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
12RELION33D reconstruction
13PHENIX1.15.2-3472model refinement
14Coot0.9-preEL(ccpem)model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3003 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063286
ELECTRON MICROSCOPYf_angle_d0.7954429
ELECTRON MICROSCOPYf_dihedral_angle_d13.691946
ELECTRON MICROSCOPYf_chiral_restr0.046475
ELECTRON MICROSCOPYf_plane_restr0.003572

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