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- EMDB-50356: Empty capsid of Rhodobacter microvirus Ebor computed with I4 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-50356
TitleEmpty capsid of Rhodobacter microvirus Ebor computed with I4 symmetry
Map datadeepEMhanced map used for the model building
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 (bacteria) / Rhodobacter phage Ebor (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBardy P / MacDonald CIW / Jenkins HT / Byrom L / Chechik M / Hart SJ / Turkenburg JP / Blaza JN / Fogg PCM / Antson AA
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust224067/Z/21/Z United Kingdom
Wellcome Trust206377 United Kingdom
Wellcome Trust109363/Z/15/A United Kingdom
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_50356.png

Downloads & links

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Map

FileDownload / File: emd_50356.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhanced map used for the model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.12897378 - 2.0406272
Average (Standard dev.)0.015900332 (±0.08853324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50356_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50356_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 B10 by sucrose ultracentrifugation
NCBI-ID: 3144506 / Sci species name: Rhodobacter phage Ebor / Sci species strain: variant S120 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Rhodobacter capsulatus (bacteria) / Strain: B10
Molecular weightTheoretical: 3.68 MDa
Virus shellShell ID: 1 / Name: Empty capsid / Diameter: 280.0 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 / Details: Ebor variant S120 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria) / Strain: B10
Molecular weightTheoretical: 55.815418 KDa
SequenceString: MSYQTKRNVR REARTLMGRF KAGKLAPVMA VPVKGSEGGM LSQSVSFELD PIAGRMATPI TAEMCAVFVP VQACDALKNP EADYAGMTE IVREKLLSGN PLFVLEPETD VSKRCGVNPR SNNGLMRVNE IVRLAHNCAV NFLRRRRYVD AVQLTAANHS T TPAILSQT ...String:
MSYQTKRNVR REARTLMGRF KAGKLAPVMA VPVKGSEGGM LSQSVSFELD PIAGRMATPI TAEMCAVFVP VQACDALKNP EADYAGMTE IVREKLLSGN PLFVLEPETD VSKRCGVNPR SNNGLMRVNE IVRLAHNCAV NFLRRRRYVD AVQLTAANHS T TPAILSQT VLDRFNGALD PDPNVNGAVQ LSMPDMRLPV ASDAEKAVTA PLTVKRGNEN RRLDAGISRL AAAEVAAATD AA LYAVFGG REAGNVSLTD FYNAQKMDEL TRVMRKICDD NPEYGEEMVL RWAHGLSVDP GRVPFLLAEK SVVLGRQIIG ATD TAGVED GVKRSDMAAQ LSFTVPIPTT ELGGIIVTFA CIKPDETLSS QPHPILADHW RLDNFVADEL ALDPQPVMAR ELDY KVAQA NETTVVFYTG LNELKKTYVS YGLCRALDPN TVESKNAVWQ LEVPLSVTPE TVLYPADLPQ YPFADQQAEV CTYVV QSTA VMPTPMIFGP SPVEQLAVIE TEDLFED

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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

BufferpH: 7.75
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMsodium chlorideNaCl
5.0 mMcalcium chlorideCaCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 2 sec, blot force 0, wait time 8 sec.
Detailsconcentration of 5x10^10 PFU/ml

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1099 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3976
Startup modelType of model: INSILICO MODEL / In silico model: autorefine model in RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 1984
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9ffg:
Empty capsid of Rhodobacter microvirus Ebor computed with I4 symmetry

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