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- PDB-7ncr: Cryo-EM structure of Pepper cryptic virus 1 VLP -

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Basic information

Entry
Database: PDB / ID: 7ncr
TitleCryo-EM structure of Pepper cryptic virus 1 VLP
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / Partitivirus / Capsid
Function / homologyviral capsid / membrane => GO:0016020 / Coat protein
Function and homology information
Biological speciesPepper cryptic virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsByrne, M.J. / Sainsbury, F. / Ranson, N.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00160X/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of Pepper Cryptic Virus 1 VLP
Authors: Byrne, M.J. / Sainsbury, F. / Ranson, N.A. / Kashyap, A. / Esquirol, L.
History
DepositionJan 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _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: Coat protein
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)95,2532
Polymers95,2532
Non-polymers00
Water00
1
A: Coat protein
B: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,715,154120
Polymers5,715,154120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Coat protein / Putative coat protein


Mass: 47626.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pepper cryptic virus 1 / Production host: Nicotiana benthamiana (plant) / References: UniProt: F8VBM8

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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: Pepper cryptic virus 1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pepper cryptic virus 1
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7
Details: 20 mM MOPS, pH 7.0 with 140 mM NaCl and 5% (v/v) glycerol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277 K

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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
Image recordingElectron dose: 1.12 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065756
ELECTRON MICROSCOPYf_angle_d0.6437852
ELECTRON MICROSCOPYf_dihedral_angle_d20.42762
ELECTRON MICROSCOPYf_chiral_restr0.047848
ELECTRON MICROSCOPYf_plane_restr0.0071000

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