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Yorodumi- EMDB-15833: CryoEM structure of the central filamentous region of the f1 fila... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15833 | |||||||||
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Title | CryoEM structure of the central filamentous region of the f1 filamentous bacteriophage, consisting of the major capsid protein pVIII | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Viral proteins / capsid / VIRUS | |||||||||
Function / homology | Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P Function and homology information | |||||||||
Biological species | Enterobacteria phage f1 (virus) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
Authors | Conners R / McLaren M / Gold VAM | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly. Authors: Rebecca Conners / Rayén Ignacia León-Quezada / Mathew McLaren / Nicholas J Bennett / Bertram Daum / Jasna Rakonjac / Vicki A M Gold / Abstract: Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular ...Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15833.map.gz | 51.7 MB | EMDB map data format | |
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Header (meta data) | emd-15833-v30.xml emd-15833.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15833_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_15833.png | 43.3 KB | ||
Filedesc metadata | emd-15833.cif.gz | 5.5 KB | ||
Others | emd_15833_half_map_1.map.gz emd_15833_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15833 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15833 | HTTPS FTP |
-Validation report
Summary document | emd_15833_validation.pdf.gz | 782.3 KB | Display | EMDB validaton report |
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Full document | emd_15833_full_validation.pdf.gz | 781.9 KB | Display | |
Data in XML | emd_15833_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_15833_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15833 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15833 | HTTPS FTP |
-Related structure data
Related structure data | 8b3qMC 8b3oC 8b3pC M: atomic model generated by this map C: citing same article (ref.) |
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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_15833.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1012 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15833_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15833_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Enterobacteria phage f1
Entire | Name: Enterobacteria phage f1 (virus) |
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Components |
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-Supramolecule #1: Enterobacteria phage f1
Supramolecule | Name: Enterobacteria phage f1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10863 / Sci species name: Enterobacteria phage f1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Escherichia coli (E. coli) / Strain: F+ strains |
-Macromolecule #1: Capsid protein G8P
Macromolecule | Name: Capsid protein G8P / type: protein_or_peptide / ID: 1 / Number of copies: 75 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterobacteria phage f1 (virus) |
Molecular weight | Theoretical: 5.212021 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AEGDDPAKAA FDSLQASATE MIGYAWAMVV VIVGATIGIK LFKKFTSKAS UniProtKB: Capsid protein G8P |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Wait time 5 sec., drain time 0 sec., blot force 0, blot time 4 sec.. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-8b3q: |