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- PDB-9jg6: The tail-complex structure of phage P22 -

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Basic information

Entry
Database: PDB / ID: 9jg6
TitleThe tail-complex structure of phage P22
Components
  • Endorhamnosidase
  • P22 tail accessory factor
  • Phage stabilisation protein
  • Portal protein
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal ...Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Endorhamnosidase / Portal protein / Phage stabilisation protein / P22 tail accessory factor
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsLiu, H.R. / Xiao, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: PLoS Biol / Year: 2025
Title: Structure of the scaffolding protein and portal within the bacteriophage P22 procapsid provides insights into the self-assembly process.
Authors: Hao Xiao / Wenyuan Chen / Hao Pang / Jing Zheng / Li Wang / Hao Feng / Jingdong Song / Lingpeng Cheng / Hongrong Liu /
Abstract: In the assembly pathway of tailed double-stranded DNA (dsDNA) bacteriophages and herpesviruses, a procapsid with a dodecameric portal for DNA delivery at a unique vertex is initially formed. ...In the assembly pathway of tailed double-stranded DNA (dsDNA) bacteriophages and herpesviruses, a procapsid with a dodecameric portal for DNA delivery at a unique vertex is initially formed. Appropriate procapsid assembly requires the transient presence of multiple copies of a scaffolding protein (SP), which is absent in the mature virion. However, how the SP contributes to dodecameric portal formation, facilitates portal and coat protein incorporation, and is subsequently released remains unclear because of a lack of structural information. Here, we present the structure of the SP-portal complex within the procapsid of bacteriophage P22 at 3-9 Å resolutions. The AlphaFold2-predicted SP model fits well with the density map of the complex. The SP forms trimers and tetramers that interact to yield a dome-like complex on the portal. Two SP domains mediate multimerization. Each trimer interacts with two neighboring portal subunits. The SP has a loop-hook-like structure that aids in coat protein recruitment during viral assembly. The loops of those SP subunits on the portal are positioned in clefts between adjacent portal subunits. Conformational changes in the portal during phage maturation may trigger the disassembly and release of the SP complex. Our findings provide insights into SP-assisted procapsid assembly in bacteriophage P22 and suggest that this strategy is also implemented by other dsDNA viruses, including herpesviruses.
History
DepositionSep 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Apr 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein
M: Endorhamnosidase
N: Endorhamnosidase
O: Endorhamnosidase
P: Endorhamnosidase
Q: Endorhamnosidase
R: Endorhamnosidase
S: Endorhamnosidase
T: Endorhamnosidase
U: Endorhamnosidase
V: Endorhamnosidase
W: Endorhamnosidase
X: Endorhamnosidase
Y: Endorhamnosidase
Z: Endorhamnosidase
a: Phage stabilisation protein
b: Phage stabilisation protein
c: Phage stabilisation protein
d: Phage stabilisation protein
e: Phage stabilisation protein
f: Phage stabilisation protein
g: P22 tail accessory factor
h: P22 tail accessory factor
i: P22 tail accessory factor
j: P22 tail accessory factor
k: P22 tail accessory factor
l: P22 tail accessory factor
m: P22 tail accessory factor
n: P22 tail accessory factor
o: P22 tail accessory factor
p: P22 tail accessory factor
q: P22 tail accessory factor
r: P22 tail accessory factor
s: Endorhamnosidase
v: Endorhamnosidase
w: Endorhamnosidase
x: Endorhamnosidase


Theoretical massNumber of molelcules
Total (without water)2,820,18848
Polymers2,820,18848
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein


Mass: 82829.375 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A3V9J0D3
#2: Protein
Endorhamnosidase / Tail spike protein， / Salmonella phage P22 tail-spike


Mass: 71923.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A3V9J050
#3: Protein
Phage stabilisation protein / Tail hub protein


Mass: 52512.020 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A444A1G7
#4: Protein
P22 tail accessory factor / Adaptor


Mass: 18044.959 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A444A265
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: Salmonella phage P22 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82501 / Symmetry type: POINT

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