+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19439 | |||||||||
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Title | Composite map of bacteriophage JBD30 capsid - neck complex | |||||||||
Map data | Composite map of bacteriophage JBD30 capsid-neck complex | |||||||||
Sample |
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Keywords | bacteriophage JBD30 / virion / capsid / connector / neck / portal / adaptor / stopper / tail / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information Protein of unknown function DUF935 / Protein of unknown function UCP028589 / Protein of unknown function (DUF935) / Bacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT Similarity search - Domain/homology | |||||||||
Biological species | Pseudomonas phage JBD30 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Valentova L / Fuzik T / Plevka P | |||||||||
Funding support | Czech Republic, European Union, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19439.map.gz | 2.1 GB | EMDB map data format | |
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Header (meta data) | emd-19439-v30.xml emd-19439.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
Images | emd_19439.png | 199.2 KB | ||
Filedesc metadata | emd-19439.cif.gz | 7.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19439 | HTTPS FTP |
-Validation report
Summary document | emd_19439_validation.pdf.gz | 502.7 KB | Display | EMDB validaton report |
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Full document | emd_19439_full_validation.pdf.gz | 502.3 KB | Display | |
Data in XML | emd_19439_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_19439_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19439 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19439 | HTTPS FTP |
-Related structure data
Related structure data | 8rqeMC 8rk3C 8rk4C 8rk5C 8rk6C 8rk7C 8rk8C 8rk9C 8rkaC 8rkbC 8rkcC 8rknC 8rkoC 8rkxC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19439.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of bacteriophage JBD30 capsid-neck complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Pseudomonas phage JBD30
Entire | Name: Pseudomonas phage JBD30 (virus) |
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Components |
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-Supramolecule #1: Pseudomonas phage JBD30
Supramolecule | Name: 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 |
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Host (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: BAA-28 |
Molecular weight | Theoretical: 20.19 MDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Mu-like prophage FluMu N-terminal domain-containing protein
Macromolecule | Name: 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 |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 12.112113 KDa |
Sequence | String: MARQNSAAKT TAKSKTDPAT EKPKDDTLPD STDDASPTAP ETPATKPDSA SDEVEGVFVR ATVERRCRAG FCFDKEGQGF ADGVLSDEQ LEALESDPLL KVERCTFSGN QEGE UniProtKB: Mu-like prophage FluMu N-terminal domain-containing protein |
-Macromolecule #2: Bacteriophage Mu GpT domain-containing protein
Macromolecule | Name: Bacteriophage Mu GpT domain-containing protein / type: protein_or_peptide / ID: 2 / Details: major capsid protein gp38 / Number of copies: 415 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 33.69498 KDa |
Sequence | String: 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 |
-Macromolecule #3: Stopper protein
Macromolecule | Name: Stopper protein / type: protein_or_peptide / ID: 3 / Details: stopper protein gp42 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 16.990168 KDa |
Sequence | String: MSDPFDYLFL EPLLIERIRS EVPGLAIVSG VPDLATLSEQ DQPAPSAYVV YLGDETGTGA DHQGGQRAIQ TVGQQWAVVL VVHYADSSN SGEGARREAG PLLGRLVKAL TGWAPAIDVA PLARSARQSP ATYASGYLYF PLVFTARFVY PRIKSWKP UniProtKB: Uncharacterized protein |
-Macromolecule #4: Virion structural protein
Macromolecule | Name: Virion structural protein / type: protein_or_peptide / ID: 4 / Details: major tail protein gp44 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 26.983729 KDa |
Sequence | String: 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 |
-Macromolecule #5: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 5 / Details: portal protein gp32 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 57.791332 KDa |
Sequence | String: 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 |
-Macromolecule #6: DUF1320 domain-containing protein
Macromolecule | Name: DUF1320 domain-containing protein / type: protein_or_peptide / ID: 6 / Details: adaptor protein gp41 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 15.155176 KDa |
Sequence | String: MSYCTLADLI EQYSEQKIRE VSDRVNKPAT TIDTVIVDRA IADADSEIDL HLHGRYQLPL ASVPTALKRI ACGLAYANLH IVLKEENPV YKTAEHLRKL LSGIANGKLS LALDADGKPA PVANTVQISE GRNDWGADW UniProtKB: DUF1320 domain-containing protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 10 mM MgSO4, 10 mM NaCl, 50 mM Tris pH 8 | ||||||||||||
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus II | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | phage titer 10^11 PFU |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |