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- EMDB-50360: Rhodobacter microvirus Ebor attached to the outer membrane vesicle -

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Basic information

Entry
Database: EMDB / ID: EMD-50360
TitleRhodobacter microvirus Ebor attached to the outer membrane vesicle
Map dataEbor virion attached to the outer membrane vesicle
Sample
  • Virus: Rhodobacter phage Ebor (virus)
    • Protein or peptide: Major capsid protein
KeywordsssDNA virus / Microviridae / Tainavirinae / Alphaproteobacteria / Rhodobacter capsulatus / aquatic virus / jelly-roll fold / VIRUS
Biological speciesRhodobacter capsulatus SB 1003 (bacteria) / Rhodobacter phage Ebor (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 13.2 Å
AuthorsBardy P / Blaza JN / Jenkins HT / Nicholas TR / Konig HC / Alim NTB / Hart SJ / Turkenburg JP / Fogg PCM / Beatty JT / Antson AA
Funding support United Kingdom, Canada, 4 items
OrganizationGrant numberCountry
Wellcome Trust224067/Z/21/Z United Kingdom
Wellcome Trust206377 United Kingdom
Wellcome Trust109363/Z/15/A United Kingdom
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 2018-03898 Canada
CitationJournal: bioRxiv / Year: 2024
Title: A stargate mechanism of genome delivery unveiled by cryogenic electron tomography.
Authors: Pavol Bardy / Conor I W MacDonald / Paul C Kirchberger / Huw T Jenkins / Tibor Botka / Lewis Byrom / Nawshin T B Alim / Daouda A K Traore / Hannah C König / Tristan R Nicholas / Maria ...Authors: Pavol Bardy / Conor I W MacDonald / Paul C Kirchberger / Huw T Jenkins / Tibor Botka / Lewis Byrom / Nawshin T B Alim / Daouda A K Traore / Hannah C König / Tristan R Nicholas / Maria Chechik / Samuel J Hart / Johan P Turkenburg / James N Blaza / J Thomas Beatty / Paul C M Fogg / Alfred A Antson /
Abstract: Single-stranded DNA bacteriophages of the family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut ...Single-stranded DNA bacteriophages of the family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.
History
DepositionMay 23, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50360.png

Downloads & links

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Map

FileDownload / File: emd_50360.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEbor virion attached to the outer membrane vesicle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.15 Å/pix.
x 256 pix.
= 806.4 Å		3.15 Å/pix.
x 256 pix.
= 806.4 Å		3.15 Å/pix.
x 256 pix.
= 806.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25
Minimum - Maximum-8.920299999999999 - 15.377575
Average (Standard dev.)0.010287293 (±1.0001875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 806.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50360_msk_1.map
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Additional map: strongly interacting class 2

Fileemd_50360_additional_1.map
Annotationstrongly interacting class 2
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Additional map: strongly interacting class 1

Fileemd_50360_additional_2.map
Annotationstrongly interacting class 1
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Additional map: weakly interacting class 2

Fileemd_50360_additional_3.map
Annotationweakly interacting class 2
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Additional map: weakly interacting class 1

Fileemd_50360_additional_4.map
Annotationweakly interacting class 1
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Half map: #2

Fileemd_50360_half_map_1.map
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Half map: #1

Fileemd_50360_half_map_2.map
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Sample components

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Entire : Rhodobacter phage Ebor

EntireName: Rhodobacter phage Ebor (virus)
Components
  • Virus: Rhodobacter phage Ebor (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Rhodobacter phage Ebor

SupramoleculeName: Rhodobacter phage Ebor / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: purified from Rhodobacter capsulatus strain SB1003 by ion-exchange chromatography
NCBI-ID: 3144506 / Sci species name: Rhodobacter phage Ebor / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 5.7 MDa
Virus shellShell ID: 1 / Name: Native capsid / Diameter: 460.0 Å / T number (triangulation number): 1

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: SB1003
SequenceString: MSYQTKRNVR REARTLMGRF KAGKLAPVMA VPVKGSEGGM LSQSVSFELD PIAGRMATPI TAEMCAVFVP VQACDALKNP EADYAGMTEI VREKLLSGNP LFVLEPETDV SKRCGVNPRR NNGLMRVNEI VRLAHNCAVN FLRRRRYVDA VQLTAANHST TPAILSQTVL ...String:
MSYQTKRNVR REARTLMGRF KAGKLAPVMA VPVKGSEGGM LSQSVSFELD PIAGRMATPI TAEMCAVFVP VQACDALKNP EADYAGMTEI VREKLLSGNP LFVLEPETDV SKRCGVNPRR NNGLMRVNEI VRLAHNCAVN FLRRRRYVDA VQLTAANHST TPAILSQTVL DRFNGALDPD PNVNGAVQLS MPDMRLPVAS DAEKAVTAPL TVKRGNENRR LDAGISRLAA AEVAAATDAA LYAVFGGREA GNVSLTDFYN AQKMDELTRV MRKICDDNPE YGEEMVLRWA HGLSVDPGRV PFLLAEKSVV LGRQIIGATD TAGVEDGVKR SDMAAQLSFT VPIPTTELGG IIVTFACIKP DETLSSQPHP ILADHWRLDN FVADELALDP QPVMARELDY KVAQANETTV VFYTGLNELK KTYVSYGLCR ALDPNTVESK NAVWQLEVPL SVTPETVLYP ADLPQYPFAD QQAEVCTYVV QSTAVMPTPM IFGPSPVEQL AVIETEDLFE D

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 10.0 mM / Component - Name: Tris-HCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: NITROGEN / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV
Details: single side blotting, 5.5 sec blotting time, 2 sec wait time, 0 force, 0 drain time.
Detailsphage Ebor mixed with outer membrane vesicles in titre of 7x10^10 PFU/ml

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1 / Average electron dose: 1.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.2 Å / Resolution method: OTHER / Software - Name: EMAN2 / Details: FSC 0.2 CUT-OFF / Number subtomograms used: 1788
ExtractionNumber tomograms: 25 / Number images used: 1788 / Reference model: native map of Ebor derived from SPA / Method: template matching / Software - Name: EMAN2
Details: template matching was performed using EMAN2 with a reference map of Ebor generated from single particle analysis, manual deletion of bad particles
Final 3D classificationNumber classes: 4 / Software - Name: EMAN2
Details: weak class 1 = 778 particles, weak class 2 = 725 particles; strong class 1 = 153 particles; strong class 2 = 132 particles
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2
FSC plot (resolution estimation)

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