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- EMDB-2184: Structure of protozoan virus from the obligate human genitourinar... -

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Entry
Database: EMDB / ID: EMD-2184
TitleStructure of protozoan virus from the obligate human genitourinary parasite Trichomonas vaginalis
Map dataIcosahedral reconstruction of TVV1
Sample
  • Sample: TVV1 virion
  • Virus: Trichomonas vaginalis virus
Keywordscryo-TEM / image reconstruction / icosahedral reconstruction / Totiviridae / T=2 virus / Trichomonas vaginalis virus 1
Biological speciesTrichomonas vaginalis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsParent KN / Takagi Y / Cardone G / Olson NH / Ericsson M / Li Y / Fichorova RN / Nibert ML / Baker TS
CitationJournal: mBio / Year: 2013
Title: Structure of a protozoan virus from the human genitourinary parasite Trichomonas vaginalis.
Authors: Kristin N Parent / Yuko Takagi / Giovanni Cardone / Norman H Olson / Maria Ericsson / May Yang / Yujin Lee / John M Asara / Raina N Fichorova / Timothy S Baker / Max L Nibert /
Abstract: The flagellated protozoan Trichomonas vaginalis is an obligate human genitourinary parasite and the most frequent cause of sexually transmitted disease worldwide. Most clinical isolates of T. ...The flagellated protozoan Trichomonas vaginalis is an obligate human genitourinary parasite and the most frequent cause of sexually transmitted disease worldwide. Most clinical isolates of T. vaginalis are persistently infected with one or more double-stranded RNA (dsRNA) viruses from the genus Trichomonasvirus, family Totiviridae, which appear to influence not only protozoan biology but also human disease. Here we describe the three-dimensional structure of Trichomonas vaginalis virus 1 (TVV1) virions, as determined by electron cryomicroscopy and icosahedral image reconstruction. The structure reveals a T = 1 capsid comprising 120 subunits, 60 in each of two nonequivalent positions, designated A and B, as previously observed for fungal Totiviridae family members. The putative protomer is identified as an asymmetric AB dimer consistent with either decamer or tetramer assembly intermediates. The capsid surface is notable for raised plateaus around the icosahedral 5-fold axes, with canyons connecting the 2- and 3-fold axes. Capsid-spanning channels at the 5-fold axes are unusually wide and may facilitate release of the viral genome, promoting dsRNA-dependent immunoinflammatory responses, as recently shown upon the exposure of human cervicovaginal epithelial cells to either TVV-infected T. vaginalis or purified TVV1 virions. Despite extensive sequence divergence, conservative features of the capsid reveal a helix-rich fold probably derived from an ancestor shared with fungal Totiviridae family members. Also notable are mass spectrometry results assessing the virion proteins as a complement to structure determination, which suggest that translation of the TVV1 RNA-dependent RNA polymerase in fusion with its capsid protein involves -2, and not +1, ribosomal frameshifting, an uncommonly found mechanism to date.
History
DepositionSep 5, 2012-
Header (metadata) releaseOct 10, 2012-
Map releaseApr 24, 2013-
UpdateApr 24, 2013-
Current statusApr 24, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2184-tvv...

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Map

FileDownload / File: emd_2184.map.gz / Format: CCP4 / Size: 468.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of TVV1
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 3.6 / Movie #1: 3.6
Minimum - Maximum-5.95059681 - 12.89856243
Average (Standard dev.)0.09929468 (±1.24523199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions501501501
Spacing501501501
CellA=B=C: 546.09 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z501501501
origin x/y/z0.0000.0000.000
length x/y/z546.090546.090546.090
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS501501501
D min/max/mean-5.95112.8990.099

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Supplemental data

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Sample components

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Entire : TVV1 virion

EntireName: TVV1 virion
Components
  • Sample: TVV1 virion
  • Virus: Trichomonas vaginalis virus

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Supramolecule #1000: TVV1 virion

SupramoleculeName: TVV1 virion / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Trichomonas vaginalis virus

SupramoleculeName: Trichomonas vaginalis virus / type: virus / ID: 1 / Name.synonym: TVV1 / NCBI-ID: 29256 / Sci species name: Trichomonas vaginalis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: TVV1
Host (natural)Organism: Trichomonas vaginalis (eukaryote) / synonym: PROTOZOA
Virus shellShell ID: 1 / Diameter: 450 Å / T number (triangulation number): 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.6 / Details: 50 mM HEPES, pH 7.2, 0.5M NaCl, 20mM MgCl2
GridDetails: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: blot for 5 sec before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: 4.12 µm / Nominal defocus min: 0.87 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER
TemperatureMin: 90 K / Max: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at high magnification
DateApr 26, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.09 µm / Number real images: 84 / Average electron dose: 22 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Robem
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM / Number images used: 4291
Detailsthe particles were selected and preprocessed using RobEM. Image reconstruction was performed using Auto3DEM

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