|Entry||Database: EMDB / ID: EMD-23561|
|Title||CryoEM structure of T. vaginalis virus 2 capsid|
|Sample||Trichomonas vaginalis virus 2:|
|Function / homology||Capsid protein|
Function and homology information
|Biological species||Trichomonas vaginalis virus 2|
|Method||single particle reconstruction / cryo EM / Resolution: 4 Å|
|Authors||Zhou ZH / Stevens AW / Cui YX / Muratore KA / Johnson PJ|
|Funding support|| United States, 10 items |
|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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_23561.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.36 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Trichomonas vaginalis virus 2
|Entire||Name: Trichomonas vaginalis virus 2|
Details: Virus particles isolated from lysed trichomonas vaginalis
Number of components: 1
-Component #1: virus, Trichomonas vaginalis virus 2
|Virus||Name: Trichomonas vaginalis virus 2 / Class: VIRION|
Details: Virus particles isolated from lysed trichomonas vaginalis
Empty: No / Enveloped: No / Isolate: STRAIN
|Mass||Theoretical: 9.40 MDa|
|Species||Species: Trichomonas vaginalis virus 2 / Strain: 2|
|Source (natural)||Host Species: Trichomonas vaginalis G3 (eukaryote) / Host species strain: G3|
|Shell #1||Name of element: Capsid / Diameter: 430.0 Å / T number (triangulation number): 1|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Buffer solution: Sterile Solution was prepared fresh to prevent contamination.|
|Vitrification||Cryogen name: ETHANE|
Details: The grids were manually plunged into liquid ethane..
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: TFS KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 2177|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2493|
|3D reconstruction||Software: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi