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- PDB-7z90: Leishmania RNA virus 1 virion -

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Basic information

Entry
Database: PDB / ID: 7z90
TitleLeishmania RNA virus 1 virion
ComponentsCapsid protein,Major capsid protein
KeywordsVIRUS / virion / full particle
Function / homologyTotivirus coat / Totivirus coat protein / Capsid protein
Function and homology information
Biological speciesLeishmania RNA virus 1 - 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsProchazkova, M. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic20-22689S Czech Republic
Citation
Journal: Virology / Year: 2022
Title: Virion structure of Leishmania RNA virus 1.
Authors: Michaela Procházková / Tibor Füzik / Danyil Grybchuk / Vyacheslav Yurchenko / Pavel Plevka /
Abstract: The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been ...The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been determined previously, however, the structure of the LRV1 virion has not been characterized. Here we used cryo-electron microscopy and single-particle reconstruction to determine the structures of the LRV1 virion and empty particle isolated from Leishmania guyanensis to resolutions of 4.0 Å and 3.6 Å, respectively. The capsid of LRV1 is built from sixty dimers of capsid proteins organized with icosahedral symmetry. RNA genomes of totiviruses are replicated inside the virions by RNA polymerases expressed as C-terminal extensions of a sub-population of capsid proteins. Most of the virions probably contain one or two copies of the RNA polymerase, however, the location of the polymerase domains in LRV1 capsid could not be identified, indicating that it varies among particles. Importance. Every year over 200 000 people contract leishmaniasis and more than five hundred people die of the disease. The mucocutaneous form of leishmaniasis produces lesions that can destroy the mucous membranes of the nose, mouth, and throat. Leishmania parasites carrying Leishmania RNA virus 1 (LRV1) are predisposed to cause aggravated symptoms in the mucocutaneous form of leishmaniasis. Here, we present the structure of the LRV1 virion determined using cryo-electron microscopy.
History
DepositionMar 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein,Major capsid protein
B: Capsid protein,Major capsid protein


Theoretical massNumber of molelcules
Total (without water)172,8632
Polymers172,8632
Non-polymers00
Water00
1
A: Capsid protein,Major capsid protein
B: Capsid protein,Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,371,809120
Polymers10,371,809120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
  • DIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein,Major capsid protein
B: Capsid protein,Major capsid protein
x 5


  • icosahedral component
  • 10-MERIC
  • 864 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)864,31710
Polymers864,31710
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein Capsid protein,Major capsid protein


Mass: 86431.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania RNA virus 1 - 4 / References: UniProt: L7XUU7
Has protein modificationY

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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: Leishmania RNA virus 1 - 4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 9.72 MDa / Experimental value: NO
Source (natural)Organism: Leishmania RNA virus 1 - 4
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Leishmania guyanensis / Strain: MHOM/BR/75/M4147
Virus shellName: capsid / Diameter: 420 nm / Triangulation number (T number): 2
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.98 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4542

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategoryDetails
7UCSF ChimeraX1.2model fitting
12RELION3.13D reconstructiongpu
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7284
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1156 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 75 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 7SN2

7sn2


Pdb chain-ID: A / Accession code: 7SN2 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.88 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00749070
ELECTRON MICROSCOPYf_angle_d0.80966820
ELECTRON MICROSCOPYf_dihedral_angle_d17.33917445
ELECTRON MICROSCOPYf_chiral_restr0.0527435
ELECTRON MICROSCOPYf_plane_restr0.0048620

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