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- EMDB-19266: Connector complex of empty bacteriophage JBD30 particle computed ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19266
TitleConnector complex of empty bacteriophage JBD30 particle computed in C12 symmetry
Map datamain map
Sample
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: DUF1320 domain-containing protein
Keywordsbacteriophage JBD30 / virion / connector complex / portal / adaptor / empty particle / VIRUS
Function / homologyProtein of unknown function DUF935 / Portal protein of Mu bacteriophage / Bacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / Portal protein / DUF1320 domain-containing protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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_19266.png

Downloads & links

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Map

FileDownload / File: emd_19266.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.803 Å		0.83 Å/pix.
x 512 pix.
= 426.803 Å		0.83 Å/pix.
x 512 pix.
= 426.803 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.039279927 - 0.07426331
Average (Standard dev.)0.00016844615 (±0.0020818836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.8032 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19266_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_19266_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_19266_half_map_2.map
Annotationhalf map 1
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)
    • Protein or peptide: Portal protein
    • Protein or peptide: DUF1320 domain-containing protein

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Supramolecule #1: Pseudomonas phage JBD30

SupramoleculeName: Pseudomonas phage JBD30 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Phage JBD30 was propagated in P. aeruginosa strain BAA-28 and purified using CsCl gradient.
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: 874 KDa
Virus shellShell ID: 1 / Name: JBD30 capsid / Diameter: 340.0 Å / T number (triangulation number): 7

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 57.791332 KDa
SequenceString: MAQIVDVYGN PIRTQQLREP QTSRLAGLAK EFAQHPAKGL TPAKLARILV EAEQGNLQAQ AELFMDMEER DAHLFAEMSK RKRAILGLD WAVEPPRNAS AAEKADADYL HELLLDLEGL EDLLLDALDG IGHGYSCIEL EWALQGREWM PLAFHHRPQS W FQLNPEDQ ...String:
MAQIVDVYGN PIRTQQLREP QTSRLAGLAK EFAQHPAKGL TPAKLARILV EAEQGNLQAQ AELFMDMEER DAHLFAEMSK RKRAILGLD WAVEPPRNAS AAEKADADYL HELLLDLEGL EDLLLDALDG IGHGYSCIEL EWALQGREWM PLAFHHRPQS W FQLNPEDQ NELRLRDNSP AGEALQPFGW IIHRPRARSG YVARSGLFRV LAWPYLFRHY ATSDLAEMLE IYGLPIRLGK YP PGTADEE KATLLRAVTG LGHAAAGIIP ETMAIDFQQA AQGSSDPFLA MMRQSEDAIS KAVLGGTLTS TTSQSGGGAF ALG QVHNEV RHDLLASDAR QLAATLSRDL LWPLLVLNRP GSPDVRRAPR LVFDLREQAD ITSMAQSIPA LVNVGLEIPS AWVY DKLGI PQPAKNEPVL RSAAQPAILS RQHGQRVAAL ATIVGPRYGD QQALDKALAS LPAKDMQDQV NDLLAPLLEA VNRGD SETE LLGALAEAFP DMDDSALTDA LHRLLFAADT WGRLHGNLDR ID

UniProtKB: Portal protein

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Macromolecule #2: DUF1320 domain-containing protein

MacromoleculeName: DUF1320 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 15.155176 KDa
SequenceString:
MSYCTLADLI EQYSEQKIRE VSDRVNKPAT TIDTVIVDRA IADADSEIDL HLHGRYQLPL ASVPTALKRI ACGLAYANLH IVLKEENPV YKTAEHLRKL LSGIANGKLS LALDADGKPA PVANTVQISE GRNDWGADW

UniProtKB: DUF1320 domain-containing protein

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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: 10 mM 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 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: 2666
Startup modelType of model: OTHER / Details: Stochastic gradient descent
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 1142
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: 3 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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