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- PDB-8a03: Bacteriophage phiCjT23 major capsid protein trimer type 3 -

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Basic information

Entry
Database: PDB / ID: 8a03
TitleBacteriophage phiCjT23 major capsid protein trimer type 3
ComponentsMajor capsid protein P5
KeywordsVIRUS / bacteriophage / phiCjT23
Biological speciesFlavobacterium phage (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRissanen, I. / Kejzar, N. / Huiskonen, J.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution.
Authors: Nejc Kejzar / Elina Laanto / Ilona Rissanen / Vahid Abrishami / Muniyandi Selvaraj / Sylvain Moineau / Janne Ravantti / Lotta-Riina Sundberg / Juha T Huiskonen /
Abstract: The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid ...The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.
History
DepositionMay 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Major capsid protein P5
K: Major capsid protein P5
J: Major capsid protein P5


Theoretical massNumber of molelcules
Total (without water)78,5423
Polymers78,5423
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5330 Å2
ΔGint-27 kcal/mol
Surface area30620 Å2

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Components

#1: Protein Major capsid protein P5


Mass: 26180.783 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Flavobacterium phage (virus)

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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: unidentified / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified (others)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Flavobacterium johnsoniae UW101
Virus shellName: Capsid / Diameter: 600 nm / Triangulation number (T number): 21
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 15 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98641 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025571
ELECTRON MICROSCOPYf_angle_d0.4177548
ELECTRON MICROSCOPYf_dihedral_angle_d2.967750
ELECTRON MICROSCOPYf_chiral_restr0.044936
ELECTRON MICROSCOPYf_plane_restr0.002960

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