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- PDB-9ffh: Native capsid of Rhodobacter microvirus Ebor computed with I4 symmetry -

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Basic information

Entry
Database: PDB / ID: 9ffh
TitleNative capsid of Rhodobacter microvirus Ebor computed with I4 symmetry
ComponentsMajor capsid protein
KeywordsVIRUS / ssDNA virus / Microviridae / Tainavirinae / Alphaproteobacteria / Rhodobacter capsulatus / aquatic virus / jelly-roll fold
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBardy, P. / MacDonald, C.I.W. / Jenkins, H.T. / Chechik, M. / Hart, S.J. / Turkenburg, J.P. / Blaza, J.N. / Fogg, P.C.M. / Antson, A.A.
Funding support United Kingdom, 3items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)55,8861
Polymers55,8861
Non-polymers00
Water00
1
B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein

B: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)3,353,13260
Polymers3,353,13260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Major capsid protein


Mass: 55885.539 Da / Num. of mol.: 1 / Mutation: variant R120 / Source method: isolated from a natural source / Details: Ebor variant R120 / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / Strain: SB1003

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rhodobacter phage Ebor / Type: VIRUS
Details: purified from Rhodobacter capsulatus strain SB1003 by CsCl ultracentrifugation
Entity ID: all / Source: NATURAL
Molecular weightValue: 5.7 MDa / Experimental value: NO
Source (natural)Organism: Rhodobacter phage Ebor (virus) / Strain: variant R120
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Rhodobacter capsulatus / Strain: SB1003
Virus shellName: Native capsid / Diameter: 460 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.75
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl1
2100 mMsodium chlorideNaCl1
35 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: concentration between 10^10-11 PFU/ml
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K / Details: blot time 2 sec, blot force 0, wait time 8 sec

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 996

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.9.8.5model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.1.3D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5271
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4935 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Related entry - empty capsid / Source name: Other / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00335420
ELECTRON MICROSCOPYf_angle_d0.61848280
ELECTRON MICROSCOPYf_dihedral_angle_d11.65713250
ELECTRON MICROSCOPYf_chiral_restr0.0465610
ELECTRON MICROSCOPYf_plane_restr0.0056380

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