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Yorodumi- EMDB-29487: Pseudomonas phage E217 neck (portal, head-to-tail connector, coll... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29487 | |||||||||
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Title | Pseudomonas phage E217 neck (portal, head-to-tail connector, collar and gateway proteins) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | pseudomonas / phage / E217 / VIRUS | |||||||||
Function / homology | Function and homology information Protein of unknown function DUF4054 / Inorganic pyrophosphatase domain / Protein of unknown function (DUF4054) / Inorganic Pyrophosphatase / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like Similarity search - Domain/homology | |||||||||
Biological species | Pseudomonas phage vB_PaeM_E217 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Li F / Cingolani G / Hou C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217. Authors: Fenglin Li / Chun-Feng David Hou / Ravi K Lokareddy / Ruoyu Yang / Francesca Forti / Federica Briani / Gino Cingolani / Abstract: E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after ...E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29487.map.gz | 407.9 MB | EMDB map data format | |
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Header (meta data) | emd-29487-v30.xml emd-29487.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29487_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_29487.png | 110 KB | ||
Filedesc metadata | emd-29487.cif.gz | 5.6 KB | ||
Others | emd_29487_half_map_1.map.gz emd_29487_half_map_2.map.gz | 410.3 MB 411.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29487 | HTTPS FTP |
-Validation report
Summary document | emd_29487_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_29487_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_29487_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_29487_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29487 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29487 | HTTPS FTP |
-Related structure data
Related structure data | 8fvhMC 8envC 8eonC 8frsC 8fuvC 8fvgC 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_29487.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29487_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29487_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pseudomonas phage vB_PaeM_E217
Entire | Name: Pseudomonas phage vB_PaeM_E217 (virus) |
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Components |
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-Supramolecule #1: Pseudomonas phage vB_PaeM_E217
Supramolecule | Name: Pseudomonas phage vB_PaeM_E217 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2034346 / Sci species name: Pseudomonas phage vB_PaeM_E217 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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-Macromolecule #1: E217 collar protein gp28
Macromolecule | Name: E217 collar protein gp28 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage vB_PaeM_E217 (virus) |
Molecular weight | Theoretical: 14.234122 KDa |
Sequence | String: IPGANLLRMA FGVIGTQIVR YRKFEQRVKN DQAQYVSMFG EPFDLAASVQ RVRRDQYAQF NLEFQRNYVM IFANFDMVDL DRNMAGDQF LWTGRVFQLE SQGSWFYQDG WGVCLAVDIG AAKA UniProtKB: Virion protein |
-Macromolecule #2: E217 gateway protein gp29
Macromolecule | Name: E217 gateway protein gp29 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage vB_PaeM_E217 (virus) |
Molecular weight | Theoretical: 21.057492 KDa |
Sequence | String: MFDGELIAKL VVELNAAMTS AQEALQFPDF EVVQKAQPTQ QGTSTRPTIF FQKLFDIPRG WPATDWHLDN TARKYVEITR QHVETTFQI SSLHWQNPEI THVVTASDIA NYVRAYFQAR STIERVKELD FLILRVSQIS NEAFENDNHQ FEFHPSFDMV V TYNQYIRL YENAAYSADG VLIG UniProtKB: Phage protein |
-Macromolecule #3: E217 head-to-tail connector protein gp27
Macromolecule | Name: E217 head-to-tail connector protein gp27 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage vB_PaeM_E217 (virus) |
Molecular weight | Theoretical: 16.885285 KDa |
Sequence | String: MVIFDEHKFR TLFPEFADPA AYPDVRLQMY FDIACEFISD RDSPYRILNG KALEACLYLL TAHLLSLSTM QVQGAAGGGV TAGGTQGGF ITSATVGEVS VAKLAPPAKN GWQWWLSGTP YGQELWALLS VKAVGGFYIG GLPERRGFRK VGGTFW UniProtKB: Phage protein |
-Macromolecule #4: E217 portal protein gp19
Macromolecule | Name: E217 portal protein gp19 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage vB_PaeM_E217 (virus) |
Molecular weight | Theoretical: 48.635984 KDa |
Sequence | String: PTMLQDWYNS QGFIGYQACA IISQHWLVDK ACSMSGEDAA RNGWELKSDG RKLSDEQSAL IARRDMEFRV KDNLVELNRF KNVFGVRIA LFVVESDDPD YYEKPFNPDG VTPGSYKGIS QIDPYWAMPQ LTAGSTADPS SEHFYEPDFW IISGKKYHRS H LVVVRGPQ ...String: PTMLQDWYNS QGFIGYQACA IISQHWLVDK ACSMSGEDAA RNGWELKSDG RKLSDEQSAL IARRDMEFRV KDNLVELNRF KNVFGVRIA LFVVESDDPD YYEKPFNPDG VTPGSYKGIS QIDPYWAMPQ LTAGSTADPS SEHFYEPDFW IISGKKYHRS H LVVVRGPQ PPDILKPTYI FGGIPLTQRI YERVYAAERT ANEAPLLAMS KRTSTIHVDV EKAIANEEAF NARLAFWIAN RD NHGVKVL GIDEGMEQFD TNLADFDSII MNQYQLVAAI AKTPATKLLG TSPKGFNATG EHETISYHEE LESIQEHIFD PLL ERHYLL LAKSEEIDVQ LEIVWNPVDS TSSQQQAELN NKKAATDEIY INSGVVSPDE VRERLRDDPR SGYNRLTDDQ AETE PGMSP ENLAEFEKAG AQSAKAKGEA ERAEAQAG UniProtKB: Inorganic pyrophosphatase 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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |