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- PDB-9cuy: Bacteriophage PhiTE extended baseplate -

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Basic information

Entry
Database: PDB / ID: 9cuy
TitleBacteriophage PhiTE extended baseplate
Components
  • Hub protein
  • Putative baseplate assembly protein
  • Putative tail fiber protein
  • Putative tape measure protein
  • Sheath initiator protein
  • Short tail fiber
  • Spacer protein
  • Tail sheath protein
  • Tail tube protein
  • Tube initiator protein
  • Wedge 1 protein
  • Wedge 2 protein
KeywordsVIRAL PROTEIN / baseplate / Sheath / Tube / PhiTE / Virus / Phage / sheath initiator / tube initiator / hub / puncture apparatus / fibers / wedge / tape measure protein
Function / homology
Function and homology information


virus tail, fiber / viral tail assembly / virion attachment to host cell
Similarity search - Function
: / : / Dit-like phage tail protein / Cyanophage baseplate Pam3 plug gp18 / Tape measure protein N-terminal / Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Tape measure protein / Phage tail collar domain / Phage tail collar domain superfamily ...: / : / Dit-like phage tail protein / Cyanophage baseplate Pam3 plug gp18 / Tape measure protein N-terminal / Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Tape measure protein / Phage tail collar domain / Phage tail collar domain superfamily / Phage protein Gp138 N-terminal domain / Phage Tail Collar Domain / Phage protein Gp138 N-terminal domain / Structural protein ORF10, bacteriophage KPP10 / Bacteriophage KPP10, Structural protein ORF10 / : / Vgr protein, OB-fold domain superfamily / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Structural protein / Putative tape measure protein / Uncharacterized protein / Structural protein / Putative baseplate assembly protein / Cyanophage baseplate Pam3 plug gp18 domain-containing protein / Uncharacterized protein / Dit-like phage tail protein N-terminal domain-containing protein / Putative baseplate assembly protein / Tail protein ...Structural protein / Putative tape measure protein / Uncharacterized protein / Structural protein / Putative baseplate assembly protein / Cyanophage baseplate Pam3 plug gp18 domain-containing protein / Uncharacterized protein / Dit-like phage tail protein N-terminal domain-containing protein / Putative baseplate assembly protein / Tail protein / Uncharacterized protein / Putative tail fiber protein
Similarity search - Component
Biological speciesPectobacterium phage phiTE (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsHodgkinson-Bean, J. / Ayala, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Global structural survey of the flagellotropic myophage φTE infecting agricultural pathogen Pectobacterium atrosepticum.
Authors: James Hodgkinson-Bean / Rafael Ayala / Nadishka Jayawardena / Georgia L Rutter / Bridget N J Watson / David Mayo-Muñoz / James Keal / Peter C Fineran / Matthias Wolf / Mihnea Bostina /
Abstract: Bacteriophages offer a promising alternative to drug-based treatments due to their effectiveness and host specificity. This is particularly important in agriculture as a biocontrol agent of plant ...Bacteriophages offer a promising alternative to drug-based treatments due to their effectiveness and host specificity. This is particularly important in agriculture as a biocontrol agent of plant diseases. Phage engineering is facilitated by structural knowledge. However, structural information regarding bacteriophages infecting plant pathogens is limited. Here, we present the cryo-EM structure of bacteriophage φTE that infects plant pathogen Pectobacterium atrosepticum. The structure reveals a distinct neck topology compared with other myophages, where tail terminator proteins compensate for reduced connectivity between sheath subunits. A contact network between tail fibers, the sheath initiator, and baseplate wedge proteins provides insights into triggers that transduce conformational changes from the baseplate to the sheath to orchestrate contraction. We observe two distinct oligomeric states of the tape measure protein (TMP), which is six-fold in regions proximal to the N-terminus and throughout most of the tail, while three-fold at the C-terminus, indicating that the TMP may be proteolytically cleaved. Our results provide a structural atlas of the model bacteriophage φTE, enhancing future interpretation of phage host interactions in pectobacteria. We anticipate that our structure will inform rational design of biocontrol agents against plant pathogens that cause diseases such as soft rot and blackleg disease in potatoes.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Wedge 2 protein
S: Wedge 2 protein
A: Tail sheath protein
C: Tail sheath protein
E: Tail sheath protein
J: Tail tube protein
H: Tail tube protein
B: Tail sheath protein
D: Tail sheath protein
F: Tail sheath protein
I: Tail tube protein
G: Tail tube protein
K: Tube initiator protein
L: Tube initiator protein
X: Hub protein
Y: Putative baseplate assembly protein
O: Wedge 1 protein
R: Wedge 2 protein
P: Wedge 1 protein
U: Wedge 2 protein
N: Spacer protein
M: Spacer protein
n: Sheath initiator protein
m: Sheath initiator protein
g: Putative tail fiber protein
i: Putative tail fiber protein
h: Putative tail fiber protein
c: Short tail fiber
a: Short tail fiber
b: Short tail fiber
W: Putative tape measure protein
j: Putative tail fiber protein
k: Putative tail fiber protein
l: Putative tail fiber protein
f: Short tail fiber
d: Short tail fiber
e: Short tail fiber


Theoretical massNumber of molelcules
Total (without water)1,751,67437
Polymers1,751,67437
Non-polymers00
Water00
1
T: Wedge 2 protein
S: Wedge 2 protein
A: Tail sheath protein
C: Tail sheath protein
E: Tail sheath protein
J: Tail tube protein
H: Tail tube protein
B: Tail sheath protein
D: Tail sheath protein
F: Tail sheath protein
I: Tail tube protein
G: Tail tube protein
K: Tube initiator protein
L: Tube initiator protein
X: Hub protein
Y: Putative baseplate assembly protein
O: Wedge 1 protein
R: Wedge 2 protein
P: Wedge 1 protein
U: Wedge 2 protein
N: Spacer protein
M: Spacer protein
n: Sheath initiator protein
m: Sheath initiator protein
g: Putative tail fiber protein
i: Putative tail fiber protein
h: Putative tail fiber protein
c: Short tail fiber
a: Short tail fiber
b: Short tail fiber
W: Putative tape measure protein
j: Putative tail fiber protein
k: Putative tail fiber protein
l: Putative tail fiber protein
f: Short tail fiber
d: Short tail fiber
e: Short tail fiber

T: Wedge 2 protein
S: Wedge 2 protein
A: Tail sheath protein
C: Tail sheath protein
E: Tail sheath protein
J: Tail tube protein
H: Tail tube protein
B: Tail sheath protein
D: Tail sheath protein
F: Tail sheath protein
I: Tail tube protein
G: Tail tube protein
K: Tube initiator protein
L: Tube initiator protein
X: Hub protein
Y: Putative baseplate assembly protein
O: Wedge 1 protein
R: Wedge 2 protein
P: Wedge 1 protein
U: Wedge 2 protein
N: Spacer protein
M: Spacer protein
n: Sheath initiator protein
m: Sheath initiator protein
g: Putative tail fiber protein
i: Putative tail fiber protein
h: Putative tail fiber protein
c: Short tail fiber
a: Short tail fiber
b: Short tail fiber
W: Putative tape measure protein
j: Putative tail fiber protein
k: Putative tail fiber protein
l: Putative tail fiber protein
f: Short tail fiber
d: Short tail fiber
e: Short tail fiber

T: Wedge 2 protein
S: Wedge 2 protein
A: Tail sheath protein
C: Tail sheath protein
E: Tail sheath protein
J: Tail tube protein
H: Tail tube protein
B: Tail sheath protein
D: Tail sheath protein
F: Tail sheath protein
I: Tail tube protein
G: Tail tube protein
K: Tube initiator protein
L: Tube initiator protein
X: Hub protein
Y: Putative baseplate assembly protein
O: Wedge 1 protein
R: Wedge 2 protein
P: Wedge 1 protein
U: Wedge 2 protein
N: Spacer protein
M: Spacer protein
n: Sheath initiator protein
m: Sheath initiator protein
g: Putative tail fiber protein
i: Putative tail fiber protein
h: Putative tail fiber protein
c: Short tail fiber
a: Short tail fiber
b: Short tail fiber
W: Putative tape measure protein
j: Putative tail fiber protein
k: Putative tail fiber protein
l: Putative tail fiber protein
f: Short tail fiber
d: Short tail fiber
e: Short tail fiber


Theoretical massNumber of molelcules
Total (without water)5,255,023111
Polymers5,255,023111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

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Protein , 12 types, 37 molecules TSRUACEBDFJHIGKLXYOPNMnmgihjkl...

#1: Protein
Wedge 2 protein / Wedge 2


Mass: 54432.738 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L596
#2: Protein
Tail sheath protein


Mass: 50647.766 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L4E9
#3: Protein
Tail tube protein


Mass: 16792.850 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L3Y2
#4: Protein Tube initiator protein


Mass: 31720.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L594
#5: Protein Hub protein


Mass: 36545.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L5R2
#6: Protein Putative baseplate assembly protein


Mass: 26474.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L4F2
#7: Protein Wedge 1 protein


Mass: 18869.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L561
#8: Protein Spacer protein


Mass: 13055.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L557
#9: Protein Sheath initiator protein


Mass: 18823.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L3Y6
#10: Protein
Putative tail fiber protein


Mass: 81935.617 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L5R6
#11: Protein
Short tail fiber


Mass: 59236.000 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L5R4
#12: Protein Putative tape measure protein


Mass: 87898.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L3Y4

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Details

Has protein modificationN

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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: Pectobacterium phage phiTE / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pectobacterium atrosepticum
Virus shellDiameter: 1000 nm / Triangulation number (T number): 13
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 4 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16480 / Symmetry type: POINT

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