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- PDB-9ilp: Structure of the bacteriophage T5 portal complex -

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Basic information

Entry
Database: PDB / ID: 9ilp
TitleStructure of the bacteriophage T5 portal complex
Components
  • Head completion protein
  • Portal protein pb7
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


cytoplasmic icosahedral capsid assembly / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral capsid assembly / virion component / viral capsid / host cell cytoplasm
Similarity search - Function
Bacteriophage/Gene transfer agent portal protein / Phage portal protein
Similarity search - Domain/homology
Portal protein / Head completion protein
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 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: Head completion protein
b: Head completion protein
c: Head completion protein
d: Head completion protein
e: Head completion protein
f: Head completion protein
g: Head completion protein
h: Head completion protein
i: Head completion protein
j: Head completion protein
k: Head completion protein
l: Head completion protein
A: Portal protein pb7
B: Portal protein pb7
C: Portal protein pb7
D: Portal protein pb7
E: Portal protein pb7
F: Portal protein pb7
G: Portal protein pb7
H: Portal protein pb7
I: Portal protein pb7
J: Portal protein pb7
K: Portal protein pb7
L: Portal protein pb7


Theoretical massNumber of molelcules
Total (without water)772,43024
Polymers772,43024
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
Head completion protein / Adaptor protein p144 / HCP / p144


Mass: 19231.912 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGD9
#2: Protein
Portal protein pb7 / Capsid protein pb7


Mass: 45137.234 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGD5

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18398 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00352092
ELECTRON MICROSCOPYf_angle_d0.66570464
ELECTRON MICROSCOPYf_dihedral_angle_d6.0446984
ELECTRON MICROSCOPYf_chiral_restr0.0848040
ELECTRON MICROSCOPYf_plane_restr0.0059096

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