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- EMDB-19439: Composite map of bacteriophage JBD30 capsid - neck complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19439
TitleComposite map of bacteriophage JBD30 capsid - neck complex
Map dataComposite map of bacteriophage JBD30 capsid-neck complex
Sample
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: Mu-like prophage FluMu N-terminal domain-containing protein
    • Protein or peptide: Bacteriophage Mu GpT domain-containing protein
    • Protein or peptide: Stopper protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Portal protein
    • Protein or peptide: DUF1320 domain-containing protein
Keywordsbacteriophage JBD30 / virion / capsid / connector / neck / portal / adaptor / stopper / tail / VIRAL PROTEIN
Function / homology
Function and homology information


Phage tail terminator protein / Protein of unknown function UCP028589 / Protein of unknown function DUF935 / Portal protein of Mu bacteriophage / Bacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT
Similarity search - Domain/homology
Portal protein / Uncharacterized protein / Bacteriophage Mu GpT domain-containing protein / Mu-like prophage FluMu N-terminal domain-containing protein / Virion structural protein / DUF1320 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas phage JBD30 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 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
DepositionJan 18, 2024-
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_19439.png

Downloads & links

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Map

FileDownload / File: emd_19439.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of bacteriophage JBD30 capsid-neck complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 840 pix.
= 873.6 Å		1.04 Å/pix.
x 840 pix.
= 873.6 Å		1.04 Å/pix.
x 840 pix.
= 873.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.0126868775 - 0.04797755
Average (Standard dev.)0.00054501626 (±0.0022112497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions840840840
Spacing840840840
CellA=B=C: 873.6 Å
α=β=γ: 90.0 °

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Supplemental data

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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: Mu-like prophage FluMu N-terminal domain-containing protein
    • Protein or peptide: Bacteriophage Mu GpT domain-containing protein
    • Protein or peptide: Stopper protein
    • Protein or peptide: Virion structural protein
    • 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: 20.19 MDa
Virus shellShell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: Mu-like prophage FluMu N-terminal domain-containing protein

MacromoleculeName: Mu-like prophage FluMu N-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Details: Minor capsid protein gp39 / Number of copies: 420 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 12.112113 KDa
SequenceString:
MARQNSAAKT TAKSKTDPAT EKPKDDTLPD STDDASPTAP ETPATKPDSA SDEVEGVFVR ATVERRCRAG FCFDKEGQGF ADGVLSDEQ LEALESDPLL KVERCTFSGN QEGE

UniProtKB: Mu-like prophage FluMu N-terminal domain-containing protein

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Macromolecule #2: Bacteriophage Mu GpT domain-containing protein

MacromoleculeName: Bacteriophage Mu GpT domain-containing protein / type: protein_or_peptide / ID: 2 / Details: major capsid protein gp38 / Number of copies: 415 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 33.69498 KDa
SequenceString: MAIITPALIS ALKTSFQKHF QDALATAPST YLQVATVIPS TTASNTYGWL GQFPKLREWI GQRVIKDMAA QGYQITNKLF ESTVGVKRT DIEDDNLGVY GPLMQEMGRA AGAHPDELVF ALLKAGNANL CYDGQNFFDT DHPVYPNVDG TGTATTVSNL F APAADPGA ...String:
MAIITPALIS ALKTSFQKHF QDALATAPST YLQVATVIPS TTASNTYGWL GQFPKLREWI GQRVIKDMAA QGYQITNKLF ESTVGVKRT DIEDDNLGVY GPLMQEMGRA AGAHPDELVF ALLKAGNANL CYDGQNFFDT DHPVYPNVDG TGTATTVSNL F APAADPGA AWYLLDTSRS LKPLIYQERM KPSFTSMTKE DDEQVFMADE YRYGVRSRCN VGFGFWQLAA MSTEELNQVN FE KVYDAMR NQKADGGRPL DIRPNLLVVP TTLRSKAKEV VGVQRLANGA DNPNFELVQV LDTAWLN

UniProtKB: Bacteriophage Mu GpT domain-containing protein

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Macromolecule #3: Stopper protein

MacromoleculeName: Stopper protein / type: protein_or_peptide / ID: 3 / Details: stopper protein gp42 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 16.990168 KDa
SequenceString:
MSDPFDYLFL EPLLIERIRS EVPGLAIVSG VPDLATLSEQ DQPAPSAYVV YLGDETGTGA DHQGGQRAIQ TVGQQWAVVL VVHYADSSN SGEGARREAG PLLGRLVKAL TGWAPAIDVA PLARSARQSP ATYASGYLYF PLVFTARFVY PRIKSWKP

UniProtKB: Uncharacterized protein

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Macromolecule #4: Virion structural protein

MacromoleculeName: Virion structural protein / type: protein_or_peptide / ID: 4 / Details: major tail protein gp44 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 26.983729 KDa
SequenceString: MAQETYFYGQ GEIDAAPIVN GVLGKWRWIQ DVSAMSIQLA VEKVEHKESY SGQKALVRSF PIGKTATVNI TLHSIGPDNL ALTLYGKVV AKAAGSVTGE VLPADLVAGD VIRLANFGVS ELVITDSASS PAPLDPQYYA LRADGAYGEV QLLGLPTPAP T QPFKAAYE ...String:
MAQETYFYGQ GEIDAAPIVN GVLGKWRWIQ DVSAMSIQLA VEKVEHKESY SGQKALVRSF PIGKTATVNI TLHSIGPDNL ALTLYGKVV AKAAGSVTGE VLPADLVAGD VIRLANFGVS ELVITDSASS PAPLDPQYYA LRADGAYGEV QLLGLPTPAP T QPFKAAYE YAATKQVGMF TAPQPTVALR YKGINLAEGG APVIVELYKV ATDPLQELAL ISDGNTVAGM QISGGILLDT SK PDTGDLG RFGRIIQLG

UniProtKB: Virion structural protein

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Macromolecule #5: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 5 / Details: portal protein gp32 / Number of copies: 12 / 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 #6: DUF1320 domain-containing protein

MacromoleculeName: DUF1320 domain-containing protein / type: protein_or_peptide / ID: 6 / Details: adaptor protein gp41 / Number of copies: 12 / 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 MgSO4, 10 mM NaCl, 50 mM Tris pH 8
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
Detailsphage titer 10^11 PFU

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 11300 / Average exposure time: 5.0 sec. / Average electron dose: 30.0 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: 130000
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: 13129
Startup modelType of model: OTHER / Details: Stochastic gradient descent
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 2913
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)

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