+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Icosahedral reconstruction of bacteriophage phiCjT23 capsid | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | bacteriophage / phiCjT23 / VIRUS | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Kejzar N / Abrishami V / Selvaraj M / Huiskonen JT | |||||||||
Funding support | 1 items
| |||||||||
![]() | ![]() 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. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 1.8 GB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 28.2 KB | Display | ![]() |
Images | ![]() | 117.2 KB | ||
Masks | ![]() | 1.9 GB | ![]() | |
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() | 1.5 GB 1.6 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zzzMC ![]() 8a01C ![]() 8a02C ![]() 8a03C ![]() 8a04C ![]() 8a05C ![]() 8a06C M: atomic model generated by this map C: citing same article ( |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_15042_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15042_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : unidentified
Entire | Name: unidentified (others) |
---|---|
Components |
|
-Supramolecule #1: unidentified
Supramolecule | Name: unidentified / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 32644 / Sci species name: unidentified / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
---|---|
Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 600.0 Å / T number (triangulation number): 21 |
-Macromolecule #1: Major capsid protein P5
Macromolecule | Name: Major capsid protein P5 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.180783 KDa |
Sequence | String: MKIATITGVT KSPELQVTKA IGALILSSDV ALSALTTEKI SIYIERGNGS NVILANKVLL KDFILASTYG TENTQSDADN AMIALCELA DEGSIYLADK ESIKITLEDL ISDKRYDLHG IEEPQQTNNL FFFEQKSVAS EEFNKKIDVQ GFDLAIMTVD D SVSDLSYQ ...String: MKIATITGVT KSPELQVTKA IGALILSSDV ALSALTTEKI SIYIERGNGS NVILANKVLL KDFILASTYG TENTQSDADN AMIALCELA DEGSIYLADK ESIKITLEDL ISDKRYDLHG IEEPQQTNNL FFFEQKSVAS EEFNKKIDVQ GFDLAIMTVD D SVSDLSYQ YSNGQVVKYL PFELQTLSRD IDPIQAVLSD GKVVQGLTDR LTLPLVAVVG IEINKSQGSI INFVVRCLKT V |
-Macromolecule #2: Spike protein P13 N-terminal, capsid internal domain
Macromolecule | Name: Spike protein P13 N-terminal, capsid internal domain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.438764 KDa |
Sequence | String: MNFIQYIDDS YAVKVKEINS SEGFYINGIQ TPFFILSVFI GNKRVTGVEF NNYDSLPMLS VINDLGNIDL NVIPQNYFAT AFTEIYFNI PF |
-Macromolecule #3: Unknown vertex protein
Macromolecule | Name: Unknown vertex protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 443.539 Da |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.2 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TECNAI ARCTICA |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.3 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
---|---|
Output model | ![]() PDB-7zzz: |