|Entry||Database: PDB / ID: 7lwy|
|Title||TVV viral capsid protein|
|Keywords||VIRAL PROTEIN / Capsid|
|Function / homology||Capsid protein|
Function and homology information
|Biological species||Trichomonas vaginalis virus 2|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å|
|Authors||Zhou, Z.H. / Stevens, A.W. / Cui, Y.X. / Johnson, P.J. / Muratore, K.A.|
|Funding support|| United States, 10items |
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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B: Capsid protein
A: Capsid protein
B: Capsid proteinx 5
A: Capsid protein
|Symmetry||Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic))|
Mass: 74037.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis virus 2 / References: UniProt: Q9JE95
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Trichomonas vaginalis virus 2 / Type: VIRUS|
Details: Virus particles isolated from lysed trichomonas vaginalis
Entity ID: #1 / Source: NATURAL
|Molecular weight||Value: 9.40 MDa / Experimental value: NO|
|Source (natural)||Organism: Trichomonas vaginalis virus 2 / Strain: 2|
|Details of virus||Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION|
|Natural host||Organism: Trichomonas vaginalis G3 / Strain: G3|
|Virus shell||Name: Capsid / Diameter: 430 nm / Triangulation number (T number): 1|
|Buffer solution||pH: 7.4 |
Details: Sterile Solution was prepared fresh to prevent contamination.
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid type: PELCO Ultrathin Carbon with Lacey Carbon|
|Vitrification||Cryogen name: ETHANE|
Details: The grids were manually plunged into liquid ethane.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: TFS KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 0.2 sec. / Electron dose: 17 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2177|
|EM imaging optics||Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV|
|Image scans||Width: 3838 / Height: 3710 / Movie frames/image: 30|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 5076|
|Symmetry||Point symmetry: C5 (5 fold cyclic)|
|3D reconstruction||Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29916 / Num. of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Protocol: AB INITIO MODEL / Space: REAL|
Details: Model was manually built into EM map using Coot, then PHENIX was used for real-space refinement
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