+
Open data
-
Basic information
Entry | Database: PDB / ID: 8bfk | ||||||
---|---|---|---|---|---|---|---|
Title | Jumbo Phage phi-kp24 tail inner tube | ||||||
![]() | Putative virion structural protein | ||||||
![]() | STRUCTURAL PROTEIN / Jumbo Phage / Klebsiella pneumoniae / tail / sheath | ||||||
Function / homology | Putative virion structural protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Ouyang, R. / Briegel, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Authors: Ruochen Ouyang / Ana Rita Costa / C Keith Cassidy / Aleksandra Otwinowska / Vera C J Williams / Agnieszka Latka / Phill J Stansfeld / Zuzanna Drulis-Kawa / Yves Briers / Daniël M Pelt / ...Authors: Ruochen Ouyang / Ana Rita Costa / C Keith Cassidy / Aleksandra Otwinowska / Vera C J Williams / Agnieszka Latka / Phill J Stansfeld / Zuzanna Drulis-Kawa / Yves Briers / Daniël M Pelt / Stan J J Brouns / Ariane Briegel / ![]() ![]() ![]() ![]() ![]() Abstract: The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein ...The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 134.3 KB | Display | |
Data in CIF | ![]() | 205.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15669MC ![]() 8au1C ![]() 8bflC ![]() 8bfpC 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: 31854.854 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Jumbo Phage phi-kp24 tail inner tube / Type: COMPLEX Details: The inner tube of Jumbo Phage phi-kp24 tail in extension Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: YES / Isolate: OTHER |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 20.89 ° / Axial rise/subunit: 39.03 Å / Axial symmetry: C6 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81869 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
|