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- PDB-7eyb: core proteins -

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Basic information

Entry
Database: PDB / ID: 7eyb
Titlecore proteins
Components
  • Internal virion protein gp14
  • Internal virion protein gp15
  • Peptidoglycan transglycosylase gp16
KeywordsVIRAL PROTEIN / bacteriophage T7 core proteins / VIRUS
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope / host cell periplasmic space / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / peptidoglycan metabolic process / symbiont entry into host / virion component ...symbiont genome ejection through host cell envelope / host cell periplasmic space / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / peptidoglycan metabolic process / symbiont entry into host / virion component / killing of cells of another organism / hydrolase activity / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function
Internal virion protein Gp16 / Internal virion protein Gp14 / Internal virion protein Gp15 / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Internal virion protein gp14 / Internal virion protein gp15 / Peptidoglycan transglycosylase gp16
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 visualization

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Assembly

Deposited unit
a: Internal virion protein gp14
b: Internal virion protein gp14
c: Internal virion protein gp14
d: Internal virion protein gp14
e: Internal virion protein gp14
f: Internal virion protein gp14
g: Internal virion protein gp14
h: Internal virion protein gp14
A: Internal virion protein gp15
B: Internal virion protein gp15
C: Internal virion protein gp15
D: Internal virion protein gp15
E: Internal virion protein gp15
F: Internal virion protein gp15
G: Internal virion protein gp15
H: Internal virion protein gp15
I: Peptidoglycan transglycosylase gp16
J: Peptidoglycan transglycosylase gp16
K: Peptidoglycan transglycosylase gp16
L: Peptidoglycan transglycosylase gp16


Theoretical massNumber of molelcules
Total (without water)1,419,67220
Polymers1,419,67220
Non-polymers00
Water00
1


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

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Components

#1: Protein
Internal virion protein gp14 / Gene product 14 / Gp14


Mass: 20990.842 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03724
#2: Protein
Internal virion protein gp15 / Gene product 15 / Gp15


Mass: 84454.008 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P03725
#3: Protein
Peptidoglycan transglycosylase gp16 / Internal core protein gp16


Mass: 144028.219 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus)
References: UniProt: P03726, Lyases; Carbon-oxygen lyases; Acting on polysaccharides

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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: 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: 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

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74984 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00579360
ELECTRON MICROSCOPYf_angle_d0.989107068
ELECTRON MICROSCOPYf_dihedral_angle_d14.81848920
ELECTRON MICROSCOPYf_chiral_restr0.04611812
ELECTRON MICROSCOPYf_plane_restr0.00614224

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