[English] 日本語
![](img/lk-miru.gif)
- EMDB-14092: Tail barrel assembly of the phicrAss001 virion with C12 symmetry ... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tail barrel assembly of the phicrAss001 virion with C12 symmetry imposed | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
Function / homology | ![]() virus tail / biological process involved in interaction with host / host cell membrane / viral life cycle / virion component / viral capsid / symbiont entry into host cell / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.21 Å | |||||||||
![]() | Bayfield OW / Shkoporov AN / Yutin N / Khokhlova EV / Smith JLR / Hawkins DEDP / Koonin EV / Hill C / Antson AA | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural atlas of a human gut crassvirus. Authors: Oliver W Bayfield / Andrey N Shkoporov / Natalya Yutin / Ekaterina V Khokhlova / Jake L R Smith / Dorothy E D P Hawkins / Eugene V Koonin / Colin Hill / Alfred A Antson / ![]() ![]() ![]() Abstract: CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant ...CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses. #1: ![]() Title: Structural atlas of the most abundant human gut virus Authors: Antson A / Bayfield O / Shkoporov A / Yutin N / Khokhlova E / Smith J / Hawkins D / Koonin E / Hill C | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 121.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 25.6 KB 25.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.5 KB | Display | ![]() |
Images | ![]() | 97.3 KB | ||
Others | ![]() ![]() | 50.6 MB 200.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qojMC ![]() 7qofC ![]() 7qogC ![]() 7qohC ![]() 7qoiC ![]() 7qokC ![]() 7qolC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3941 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: #1
File | emd_14092_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #2
File | emd_14092_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : Bacteroides phage crAss001
+Supramolecule #1: Bacteroides phage crAss001
+Macromolecule #1: Portal protein gp20
+Macromolecule #2: Ring protein 1 gp43
+Macromolecule #3: Ring protein 2 gp40
+Macromolecule #4: Ring protein 3 gp35
+Macromolecule #5: Ring protein 4/5 gp34
+Macromolecule #6: Tail hub protein A gp38
+Macromolecule #7: Tail hub protein B gp39
+Macromolecule #8: Tail fiber protein gp22
+Macromolecule #9: Cargo protein 1 gp45
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 169 |
---|---|
Output model | ![]() PDB-7qoj: |