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Yorodumi- EMDB-15051: Localized reconstruction of flavobacterium infecting lipid-contai... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15051 | |||||||||
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Title | Localized reconstruction of flavobacterium infecting lipid-containing phage FLiP vertex | |||||||||
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Sample |
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Keywords | bacteriophage / Flavobacterium / lipid-containing / phage / FLiP / penton protein / VIRUS | |||||||||
Function / homology | DUF3168 domain-containing protein Function and homology information | |||||||||
Biological species | Flavobacterium phage FLiP (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Kejzar N / Abrishami V / Selvaraj M / Huiskonen JT | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution. Authors: Nejc Kejzar / Elina Laanto / Ilona Rissanen / Vahid Abrishami / Muniyandi Selvaraj / Sylvain Moineau / Janne Ravantti / Lotta-Riina Sundberg / Juha T Huiskonen / Abstract: The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid ...The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution. #1: Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Virus found in a boreal lake links ssDNA and dsDNA viruses. Authors: Laanto E / Mantynen S / De Colibus L / Marjakangas J / Gillum A / Stuart DI / Ravantti JJ / Huiskonen JT / Sundberg LR | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15051.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-15051-v30.xml emd-15051.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15051_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_15051.png | 124 KB | ||
Masks | emd_15051_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-15051.cif.gz | 5.2 KB | ||
Others | emd_15051_half_map_1.map.gz emd_15051_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15051 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15051 | HTTPS FTP |
-Validation report
Summary document | emd_15051_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_15051_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_15051_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_15051_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15051 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15051 | HTTPS FTP |
-Related structure data
Related structure data | 8a06MC 7zzzC 8a01C 8a02C 8a03C 8a04C 8a05C 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_15051.map.gz / Format: CCP4 / Size: 30.5 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: 1.35 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15051_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15051_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15051_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Flavobacterium phage FLiP
Entire | Name: Flavobacterium phage FLiP (virus) |
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Components |
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-Supramolecule #1: Flavobacterium phage FLiP
Supramolecule | Name: Flavobacterium phage FLiP / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2023716 / Sci species name: Flavobacterium phage FLiP / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Flavobacterium (bacteria) |
-Macromolecule #1: Penton protein P12
Macromolecule | Name: Penton protein P12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Flavobacterium phage FLiP (virus) |
Molecular weight | Theoretical: 16.851057 KDa |
Sequence | String: DFSTIPIDYV KAKDPNTIDF CLSYLELYHT TKAVKACTPF SFILGSDAGM QRATETTESL YWGKVILDIN PNLSPLVNTT IVLEIESML SSNSINRSEN KRITRYIEKE NFVNESSERF EFFKSMELSH LSTAYDVYVT FIGFKIDL UniProtKB: DUF3168 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: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 22.0 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: 0.7000000000000001 µm |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8a06: |