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- PDB-8bfk: Jumbo Phage phi-kp24 tail inner tube -

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Basic information

Entry
Database: PDB / ID: 8bfk
TitleJumbo Phage phi-kp24 tail inner tube
ComponentsPutative virion structural protein
KeywordsSTRUCTURAL PROTEIN / Jumbo Phage / Klebsiella pneumoniae / tail / sheath
Function / homologyPutative virion structural protein
Function and homology information
Biological speciesKlebsiella phage vB_KpM_FBKp24 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsOuyang, R. / Briegel, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)84.034.014 Netherlands
CitationJournal: 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
DepositionOct 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative virion structural protein
B: Putative virion structural protein
C: Putative virion structural protein
D: Putative virion structural protein
E: Putative virion structural protein
F: Putative virion structural protein
G: Putative virion structural protein
H: Putative virion structural protein
I: Putative virion structural protein
J: Putative virion structural protein
K: Putative virion structural protein
L: Putative virion structural protein
M: Putative virion structural protein
N: Putative virion structural protein
O: Putative virion structural protein
P: Putative virion structural protein
Q: Putative virion structural protein
R: Putative virion structural protein


Theoretical massNumber of molelcules
Total (without water)573,38718
Polymers573,38718
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Putative virion structural protein / tail inner tube


Mass: 31854.854 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage vB_KpM_FBKp24 (virus) / References: UniProt: A0A7U0GBC4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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 weightExperimental value: NO
Source (natural)Organism: Klebsiella phage vB_KpM_FBKp24 (virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
7ISOLDEmodel fitting
9PHENIXmodel refinement
13RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 20.89 ° / Axial rise/subunit: 39.03 Å / Axial symmetry: C6
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81869 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00341112
ELECTRON MICROSCOPYf_angle_d0.51755800
ELECTRON MICROSCOPYf_dihedral_angle_d4.8195688
ELECTRON MICROSCOPYf_chiral_restr0.0446102
ELECTRON MICROSCOPYf_plane_restr0.0047362

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