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- PDB-9ioz: Structure of the bacteriophage T5 tail tip complex -

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Basic information

Entry
Database: PDB / ID: 9ioz
TitleStructure of the bacteriophage T5 tail tip complex
Components
  • Baseplate hub protein pb3
  • Baseplate tube protein p140
  • Distal tail protein pb9
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


virus tail, baseplate / virus tail
Similarity search - Function
: / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain
Similarity search - Domain/homology
Baseplate tube protein p140 / Distal tail protein pb9 / Baseplate hub protein pb3
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPeng, Y.N. / Liu, H.R.
Funding support China, 4items
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)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structures of Mature and Urea-Treated Empty Bacteriophage T5: Insights into Siphophage Infection and DNA Ejection.
Authors: Yuning Peng / Huanrong Tang / Hao Xiao / Wenyuan Chen / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, ...T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, we used cryo-electron microscopy (cryo-EM) to determine the structures of mature T5 (a laboratory-adapted, fiberless T5 mutant) and urea-treated empty T5 (lacking the tip complex) at near-atomic resolutions. Atomic models of the head, connector complex, tail tube, and tail tip were built for mature T5, and atomic models of the connector complex, comprising the portal protein pb7, adaptor protein p144, and tail terminator protein p142, were built for urea-treated empty T5. Our findings revealed that the aforementioned proteins did not undergo global conformational changes before and after DNA ejection, indicating that these structural features were conserved among most myophages and siphophages. The present study elucidates the underlying mechanisms of siphophage infection and DNA ejection.
History
DepositionJul 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baseplate tube protein p140
B: Baseplate tube protein p140
C: Baseplate tube protein p140
D: Distal tail protein pb9
E: Distal tail protein pb9
F: Distal tail protein pb9
G: Distal tail protein pb9
H: Distal tail protein pb9
I: Distal tail protein pb9
J: Baseplate hub protein pb3
K: Baseplate hub protein pb3
L: Baseplate hub protein pb3


Theoretical massNumber of molelcules
Total (without water)561,73412
Polymers561,73412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Baseplate tube protein p140 / p140 / Minor tail protein p140 / Tail protein p140


Mass: 34367.605 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE3
#2: Protein
Distal tail protein pb9 / DTP-pb9 / Dit / Tail protein pb9


Mass: 22798.641 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE8
#3: Protein Baseplate hub protein pb3 / BHP-pb3 / Tail protein pb3


Mass: 107279.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE9

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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 T5 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T5 (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: 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: 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: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30589 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00537722
ELECTRON MICROSCOPYf_angle_d0.89751204
ELECTRON MICROSCOPYf_dihedral_angle_d7.1085073
ELECTRON MICROSCOPYf_chiral_restr0.0585613
ELECTRON MICROSCOPYf_plane_restr0.016660

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