[English] 日本語
![](img/lk-miru.gif)
- PDB-7ukj: In situ cryo-EM structure of bacteriophage Sf6 portal:gp7 complex... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ukj | ||||||
---|---|---|---|---|---|---|---|
Title | In situ cryo-EM structure of bacteriophage Sf6 portal:gp7 complex at 2.7A resolution | ||||||
![]() | Gene 14 protein | ||||||
![]() | VIRAL PROTEIN / in situ / phage / portal / gp7 / gp3 / structural protein | ||||||
Function / homology | ![]() virus tail / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Li, F. / Cingolani, G. / Hou, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: High-resolution cryo-EM structure of the virus Sf6 genome delivery tail machine. Authors: Fenglin Li / Chun-Feng David Hou / Ruoyu Yang / Richard Whitehead / Carolyn M Teschke / Gino Cingolani / ![]() Abstract: Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom ...Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 312.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 258 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 926 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 955.9 KB | Display | |
Data in XML | ![]() | 63.9 KB | Display | |
Data in CIF | ![]() | 96.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26582MC ![]() 7sfsC ![]() 7sg7C ![]() 7sp4C ![]() 7spuC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 67118.141 Da / Num. of mol.: 3 / Fragment: Tailspike / Source method: isolated from a natural source / Source: (natural) ![]() Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Shigella virus Sf6 / Type: VIRUS / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() |
Details of virus | Empty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7977 |
-
Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 67439 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|