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- PDB-9l0e: Cryo-EM structure of bacteriophage T1 stopper-tail terminator -

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Basic information

Entry
Database: PDB / ID: 9l0e
TitleCryo-EM structure of bacteriophage T1 stopper-tail terminator
Components
  • Tail protein
  • stopper protein
KeywordsVIRAL PROTEIN / stopper / tail terminator / phage / VIRUS PROTEIN
Function / homologyProtein of unknown function DUF4128 / Phage tail terminator protein / Tail protein / Uncharacterized protein
Function and homology information
Biological speciesEscherichia phage T1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen, Y. / Liu, H.R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: The in situ structure of T-series T1 reveals a conserved Lambda-like tail tip
Authors: Chen, Y. / Liu, H.R.
History
DepositionDec 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: Tail protein
Q: Tail protein
T: Tail protein
V: Tail protein
Y: Tail protein
b: Tail protein
A: stopper protein
B: stopper protein
C: stopper protein
D: stopper protein
E: stopper protein
G: stopper protein


Theoretical massNumber of molelcules
Total (without water)174,13812
Polymers174,13812
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
Tail protein


Mass: 15191.521 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: Q6XQC8
#2: Protein
stopper protein


Mass: 13831.523 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: Q6XQD0
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: Escherichia phage T1 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T1 (virus)
Buffer solutionpH: 7.6
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: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23461 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0112348
ELECTRON MICROSCOPYf_angle_d1.04516704
ELECTRON MICROSCOPYf_dihedral_angle_d4.5241704
ELECTRON MICROSCOPYf_chiral_restr0.0481758
ELECTRON MICROSCOPYf_plane_restr0.0062214

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