+Open data
-Basic information
Entry | Database: PDB / ID: 8bfp | ||||||
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Title | Jumbo Phage phi-kp24 empty capsid pentamer hexamers | ||||||
Components | Major head protein | ||||||
Keywords | VIRUS / Jumbo phage / Klebsiella pheumoniae / Capsid | ||||||
Function / homology | Major head protein Function and homology information | ||||||
Biological species | Klebsiella phage vB_KpM_FBKp24 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Ouyang, R. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Nat Commun / Year: 2022 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bfp.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8bfp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bfp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8bfp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8bfp_validation.xml.gz | 455.5 KB | Display | |
Data in CIF | 8bfp_validation.cif.gz | 706.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bfp ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bfp | HTTPS FTP |
-Related structure data
Related structure data | 13862MC 8au1C 8bfkC 8bflC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 63734.039 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage vB_KpM_FBKp24 (virus) / References: UniProt: A0A7U0GBA8 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Jumbo Phage phi-kp24 empty capsid pentamer hexamers / Type: COMPLEX / Details: A pentamer surrounding with five hexamers / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Klebsiella phage vB_KpM_FBKp24 (virus) |
Buffer solution | pH: 7 |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 0.053 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 19193 / Symmetry type: POINT |