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- EMDB-19263: Baseplate of bacteriophage JBD30 computed in C3 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-19263
TitleBaseplate of bacteriophage JBD30 computed in C3 symmetry
Map datamain map
Sample
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: DUF2163 domain-containing protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Tip attachment protein J domain-containing protein
  • Ligand: FE (III) ION
Keywordsbacteriophage JBD30 / virion / baseplate / distal tail protein / baseplate hub / baseplate upper protein / VIRUS
Function / homologyBacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Uncharacterized protein / Virion structural protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 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_19263.png

Downloads & links

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Map

FileDownload / File: emd_19263.map.gz / Format: CCP4 / Size: 600.7 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 540 pix.
= 450.144 Å		0.83 Å/pix.
x 540 pix.
= 450.144 Å		0.83 Å/pix.
x 540 pix.
= 450.144 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: 0.01
Minimum - Maximum-0.018793978 - 0.06754456
Average (Standard dev.)0.00024075719 (±0.0016620867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 450.14398 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19263_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_19263_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_19263_half_map_2.map
Annotationhalf_map_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: DUF2163 domain-containing protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Tip attachment protein J domain-containing protein
  • Ligand: FE (III) ION

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Supramolecule #1: Pseudomonas phage JBD30

SupramoleculeName: Pseudomonas phage JBD30 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 516 KDa
Virus shellShell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: DUF2163 domain-containing protein

MacromoleculeName: DUF2163 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 29.979053 KDa
SequenceString: MSFNSRESSL ADGQPVRLYQ FSRGAIRWSY NSSDRDITYQ NQIFRTVPGG ITDNGIICSG DPQSDQFVIT APADLDVALL YKTRSPSDA IDLVVYDMHY GDAEAAVSWV GQIGDVDWPT VDSCRITCVS EDELMDQPGL TDTYCRTCTA IVGDHRCKVN L VPYRVTLT ...String:
MSFNSRESSL ADGQPVRLYQ FSRGAIRWSY NSSDRDITYQ NQIFRTVPGG ITDNGIICSG DPQSDQFVIT APADLDVALL YKTRSPSDA IDLVVYDMHY GDAEAAVSWV GQIGDVDWPT VDSCRITCVS EDELMDQPGL TDTYCRTCTA IVGDHRCKVN L VPYRVTLT PQSVSAWVIS SGVVAGYADG WFTGGYVEWQ VDGDNYDRRF IEQHAGADLH ILGGTEGIPA GGQLRVYPGC DG LAQTCDD KFSNLPNFRG FNAMQGKSPF DGDQVW

UniProtKB: Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein

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Macromolecule #2: Virion structural protein

MacromoleculeName: Virion structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 62.163148 KDa
SequenceString: MATFPGFQVP KPVEGIVAGI TPNIDALELN QDISLAAVAA STWGGAYGAH QPVEVIHSTY QAVHQSALEE NYYNRLWLIP TAMELGNVV STQIRPASVW NAYFSPRTLT AIDREAADGI TLSGQASPPL GFAALEERTW TVSIGTDGPP VVNARIVWRL Q GEPNLVLV ...String:
MATFPGFQVP KPVEGIVAGI TPNIDALELN QDISLAAVAA STWGGAYGAH QPVEVIHSTY QAVHQSALEE NYYNRLWLIP TAMELGNVV STQIRPASVW NAYFSPRTLT AIDREAADGI TLSGQASPPL GFAALEERTW TVSIGTDGPP VVNARIVWRL Q GEPNLVLV ITGNRIIAWT FAPDWGDSIV ERLSASTNIL QSESAVTQRR AMRLAPRREF DANMYAVDRE RQLLDMTLFG WG ARIWALP IWPDIQLLHQ PLAAGSLGIP CDTAGLDFRD GGLAMLRGED AFTYEVVEVK TVTASGLDLV RPVQAAWGTG SRL YPVRTA QLTEQPTLTR LTDTAQSARV SFLVMEPSAW PELMPATTYR GRPVLEQRPD ESEDLTSSYQ RLLSTLDNGS AIPR VTDVA GMALPVIGHR WIGMGRAERS AFRSLVYALR GQQKPLWVPT HADDLTLVAT VSQLSTALDV RNIGYARFAN GRPGR RDIR IELYDGTVYH RRILTSTELD ADTERVAIDA ALGRLVEPTD VARICFMALC SAASDVVEIE HVTDSEGVAT AALTFK GVR DDEF

UniProtKB: Virion structural protein

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Macromolecule #3: Tip attachment protein J domain-containing protein

MacromoleculeName: Tip attachment protein J domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 79.898781 KDa
SequenceString: MGAKPKAQTV GWRYYFDIHF ALGKKVDEVC AIRASGKTAW KGSITSNGQV RINAPELFGG DKGEGGLDGT LDVLFGEEDQ GVLPRLAAM LGGLVPAFRG VTTCFYSGLV TSVNPYPKKW EILRRGGNRL WDGNPWYPEK QFVWLADGQI KAMNPAHILY L VYTGRDFR ...String:
MGAKPKAQTV GWRYYFDIHF ALGKKVDEVC AIRASGKTAW KGSITSNGQV RINAPELFGG DKGEGGLDGT LDVLFGEEDQ GVLPRLAAM LGGLVPAFRG VTTCFYSGLV TSVNPYPKKW EILRRGGNRL WDGNPWYPEK QFVWLADGQI KAMNPAHILY L VYTGRDFR GLARTRMDEA SWRAAADTLY AEGFGLCFEW TRSDSFKNFC ETVKSHIGAE VYPNRQTGQI SIRLLRDDYN VA DLPLFDE DSGLLEITQE KTGSTSLAPS QLIVKYIDQI DGAQRQIIVN NNAVAASQGR RSSEEIEFLG VPTGELAGRV GER EMRLKT TGLKRYKGVF DRRARSLNPG QPFLIRSTPR GIPETVVRVG RIEDNFLGDG KITLTVVQDQ FNLPATTGVA PPPP GWTPP DRTPRAITVR RLIEAPYREL AGVIDPANLQ LLDVSASYLA ALAEAPTSLS QSYTLTDRVG SSGAFVDRGT GDWCP TGLL AAELPLAAGP NVVTLTNATR LEDVTVGQAA VVDDEIVRVD AVNYASGTVT LARGCADTVP AKHLAGARVW FYDTFE AVD ETVYSQGVTL QARLLTNTSE GQLAPALAAT DSLTLTGRQG KPYPPGQFRI NGSAYPTKVY GALSVSWAKR DRIGQAD QL IDTTVGNIGP EDGATVTLQV YSGTTLKRTY AGLTSSSWSY PLAEDMADGP LQDVRLVLRS VRDGIDSWQQ HDITIERH G LGFRLGEELG GVSA

UniProtKB: Uncharacterized protein

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Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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 force 0, blotting time 2s, 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: 8376
Startup modelType of model: OTHER / Details: Stochastic gradient descent
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 1780
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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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8rk7:
Baseplate of bacteriophage JBD30 computed in C3 symmetry

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