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- PDB-8bfp: Jumbo Phage phi-kp24 empty capsid pentamer hexamers -

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Basic information

Entry
Database: PDB / ID: 8bfp
TitleJumbo Phage phi-kp24 empty capsid pentamer hexamers
ComponentsMajor head protein
KeywordsVIRUS / Jumbo phage / Klebsiella pheumoniae / Capsid
Function / homologyMajor head protein
Function and homology information
Biological speciesKlebsiella phage vB_KpM_FBKp24 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsOuyang, R.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
G: Major head protein
H: Major head protein
I: Major head protein
J: Major head protein
K: Major head protein
L: Major head protein
M: Major head protein
N: Major head protein
O: Major head protein
P: Major head protein
Q: Major head protein
R: Major head protein
S: Major head protein
T: Major head protein
U: Major head protein
V: Major head protein
W: Major head protein
X: Major head protein
Y: Major head protein
Z: Major head protein
a: Major head protein
b: Major head protein
c: Major head protein
d: Major head protein
e: Major head protein
f: Major head protein
g: Major head protein
h: Major head protein
i: Major head protein
j: Major head protein


Theoretical massNumber of molelcules
Total (without water)2,230,69135
Polymers2,230,69135
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area327700 Å2
ΔGint-839 kcal/mol
Surface area807360 Å2
MethodPISA

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Components

#1: Protein ...
Major head 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

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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 empty capsid pentamer hexamers / Type: COMPLEX / Details: A pentamer surrounding with five hexamers / Entity ID: all / Source: NATURAL
Source (natural)Organism: Klebsiella phage vB_KpM_FBKp24 (virus)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 64000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 0.053 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7ISOLDEmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 19193 / Symmetry type: POINT

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