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- PDB-7ey9: tail proteins -

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Basic information

Entry
Database: PDB / ID: 7ey9
Titletail proteins
Components
  • Tail fiber protein
  • Tail tubular protein gp11
  • Tail tubular protein gp12
KeywordsVIRAL PROTEIN / bacteriophae T7 tail proteins / VIRUS
Function / homology
Function and homology information


virus tail, tube / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
: / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein
Similarity search - Domain/homology
Tail tubular protein gp11 / Tail tubular protein gp12 / Tail fiber protein
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu, H.R. / Chen, W.Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structural changes in bacteriophage T7 upon receptor-induced genome ejection.
Authors: Wenyuan Chen / Hao Xiao / Li Wang / Xurong Wang / Zhixue Tan / Zhen Han / Xiaowu Li / Fan Yang / Zhonghua Liu / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
Abstract: Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel ...Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near-atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane.
History
DepositionMay 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
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Assembly

Deposited unit
a: Tail fiber protein
b: Tail fiber protein
c: Tail fiber protein
d: Tail fiber protein
e: Tail fiber protein
f: Tail fiber protein
g: Tail fiber protein
h: Tail fiber protein
i: Tail fiber protein
j: Tail fiber protein
k: Tail fiber protein
l: Tail fiber protein
m: Tail fiber protein
n: Tail fiber protein
o: Tail fiber protein
p: Tail fiber protein
q: Tail fiber protein
r: Tail fiber protein
s: Tail tubular protein gp12
t: Tail tubular protein gp12
u: Tail tubular protein gp12
v: Tail tubular protein gp12
w: Tail tubular protein gp12
x: Tail tubular protein gp12
M: Tail tubular protein gp11
N: Tail tubular protein gp11
O: Tail tubular protein gp11
P: Tail tubular protein gp11
Q: Tail tubular protein gp11
R: Tail tubular protein gp11
S: Tail tubular protein gp11
T: Tail tubular protein gp11
U: Tail tubular protein gp11
V: Tail tubular protein gp11
W: Tail tubular protein gp11
X: Tail tubular protein gp11


Theoretical massNumber of molelcules
Total (without water)1,914,12936
Polymers1,914,12936
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tail fiber protein / Gene product 17 / Gp17 / Tail fiber protein gp17


Mass: 61641.875 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03748
#2: Protein
Tail tubular protein gp12 / Gene product 12 / Gp12


Mass: 89480.594 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03747
#3: Protein
Tail tubular protein gp11 / Gene product 11 / Gp11


Mass: 22307.650 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03746

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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: Escherichia phage T7 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T7 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75068 / Symmetry type: POINT

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