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- EMDB-19274: Capsid of bacteriophage JBD30 computed in C5 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-19274
TitleCapsid of bacteriophage JBD30 computed in C5 symmetry
Map datamain map
Sample
  • Virus: Pseudomonas phage JBD30 (virus)
Keywordsbacteriophage JBD30 / virion / capsid / VIRUS
Biological speciesPseudomonas phage JBD30 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsValentova L / Fuzik T / Plevka P
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
European Research Council (ERC)101043452European Union
Citation
Journal: EMBO J / Year: 2024
Title: Structure and replication of Pseudomonas aeruginosa phage JBD30.
Authors: Lucie Valentová / Tibor Füzik / Jiří Nováček / Zuzana Hlavenková / Jakub Pospíšil / Pavel Plevka /
Abstract: Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection ...Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.
#1: Journal: Embo J. / Year: 2024
Title: Structure and replication of Pseudomonas aeruginosa phage JBD30
Authors: Valentova L / Plevka P / Fuzik T / Novacek J / Pospisil J
History
DepositionDec 23, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19274.png

Downloads & links

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Map

FileDownload / File: emd_19274.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 840 pix.
= 700.224 Å		0.83 Å/pix.
x 840 pix.
= 700.224 Å		0.83 Å/pix.
x 840 pix.
= 700.224 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.05600124 - 0.08210166
Average (Standard dev.)0.00032967274 (±0.0037929164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions840840840
Spacing840840840
CellA=B=C: 700.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19274_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_19274_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_19274_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage JBD30

EntireName: Pseudomonas phage JBD30 (virus)
Components
  • Virus: Pseudomonas phage JBD30 (virus)

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Supramolecule #1: Pseudomonas phage JBD30

SupramoleculeName: Pseudomonas phage JBD30 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1223260 / Sci species name: Pseudomonas phage JBD30 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: BAA-28
Molecular weightTheoretical: 13.971 MDa
Virus shellShell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7

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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: 8
Component:
ConcentrationFormulaName
10.0 mMNaClsodium chloride
10.0 mMMgSO4magnesium sulphate
50.0 mMTris-HCltris hydrochloride

Details: 10m M NaCl, 10 mM MgSO4, 50 mM Tris-HCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus II
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: blotting time 2s, blotting force 0, waiting time 15s.
Detailsphage titer of 10^11 PFU/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12356 / Average exposure time: 2.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5167
Startup modelType of model: OTHER / Details: Stochastic gradient descent
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 3567
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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