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- EMDB-23561: CryoEM structure of T. vaginalis virus 2 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-23561
TitleCryoEM structure of T. vaginalis virus 2 capsid
Map data
SampleTrichomonas vaginalis virus 2:
virus
Function / homologyCapsid protein
Function and homology information
Biological speciesTrichomonas vaginalis virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsZhou ZH / Stevens AW / Cui YX / Muratore KA / Johnson PJ
Funding support United States, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103182 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33AI119721 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007323 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: mBio / Year: 2021
Title: Atomic Structure of the Trichomonas vaginalis Double-Stranded RNA Virus 2.
Authors: Alexander Stevens / Katherine Muratore / Yanxiang Cui / Patricia J Johnson / Z Hong Zhou /
Abstract: , the causative pathogen for the most common nonviral sexually transmitted infection worldwide, is itself frequently infected with one or more of the four types of small double-stranded RNA (dsRNA) ..., the causative pathogen for the most common nonviral sexually transmitted infection worldwide, is itself frequently infected with one or more of the four types of small double-stranded RNA (dsRNA) viruses (TVV1 to 4, genus , family ). Each TVV encloses a nonsegmented genome within a single-layered capsid and replicates entirely intracellularly, like many dsRNA viruses, and unlike those in the family. Here, we have determined the structure of TVV2 by cryo-electron microscopy (cryoEM) at 3.6 Å resolution and derived an atomic model of its capsid. TVV2 has an icosahedral, T = 2*, capsid comprised of 60 copies of the icosahedral asymmetric unit (a dimer of the two capsid shell protein [CSP] conformers, CSP-A and CSP-B), typical of icosahedral dsRNA virus capsids. However, unlike the robust CSP-interlocking interactions such as the use of auxiliary "clamping" proteins among , only lateral CSP interactions are observed in TVV2, consistent with an assembly strategy optimized for TVVs' intracellular-only replication cycles within their protozoan host. The atomic model reveals both a mostly negatively charged capsid interior, which is conducive to movement of the loosely packed genome, and channels at the 5-fold vertices, which we suggest as routes of mRNA release during transcription. Structural comparison of TVV2 to the L-A virus reveals a conserved helix-rich fold within the CSP and putative guanylyltransferase domain along the capsid exterior, suggesting conserved mRNA maintenance strategies among This first atomic structure of a TVV provides a framework to guide future biochemical investigations into the interplay between and its viruses. viruses (TVVs) are double-stranded RNA (dsRNA) viruses that cohabitate in , the causative pathogen of trichomoniasis, the most common nonviral sexually transmitted disease worldwide. Featuring an unsegmented dsRNA genome encoding a single capsid shell protein (CSP), TVVs contrast with multisegmented dsRNA viruses, such as the diarrhea-causing rotavirus, whose larger genome is split into 10 dsRNA segments encoding 5 unique capsid proteins. To determine how TVVs incorporate the requisite functionalities for viral replication into their limited proteome, we derived the atomic model of TVV2, a first for TVVs. Our results reveal the intersubunit interactions driving CSP association for capsid assembly and the properties that govern organization and maintenance of the viral genome. Structural comparison between TVV2 capsids and those of distantly related dsRNA viruses indicates conserved strategies of nascent RNA release and a putative viral guanylyltransferase domain implicated in the cytoplasmic maintenance of viral messenger and genomic RNA.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMar 2, 2021-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0113
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0113
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m12
  • Surface level: 0.0113
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7m12
  • Imaged by Jmol
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23561.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 480 pix.
= 652.8 Å
1.36 Å/pix.
x 480 pix.
= 652.8 Å
1.36 Å/pix.
x 480 pix.
= 652.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.0113 / Movie #1: 0.0113
Minimum - Maximum-0.010441254 - 0.025645649
Average (Standard dev.)0.0003047758 (±0.0018689359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z652.800652.800652.800
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0100.0260.000

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Supplemental data

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Sample components

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Entire Trichomonas vaginalis virus 2

EntireName: Trichomonas vaginalis virus 2
Details: Virus particles isolated from lysed trichomonas vaginalis
Number of components: 1

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Component #1: virus, Trichomonas vaginalis virus 2

VirusName: Trichomonas vaginalis virus 2 / Class: VIRION
Details: Virus particles isolated from lysed trichomonas vaginalis
Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 9.40 MDa
SpeciesSpecies: Trichomonas vaginalis virus 2 / Strain: 2
Source (natural)Host Species: Trichomonas vaginalis G3 (eukaryote) / Host species strain: G3
Shell #1Name of element: Capsid / Diameter: 430.0 Å / T number (triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: Sterile Solution was prepared fresh to prevent contamination.
pH: 7.4
VitrificationCryogen name: ETHANE
Details: The grids were manually plunged into liquid ethane..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2177

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2493
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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