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- PDB-9l9p: Cryo-EM structure of bacteriophage T1 tail tip complex -

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Basic information

Entry
Database: PDB / ID: 9l9p
TitleCryo-EM structure of bacteriophage T1 tail tip complex
Components
  • (Putative minor tail ...) x 2
  • (Putative tail ...) x 2
  • Tape measure protein
KeywordsVIRAL PROTEIN / tail tip complex
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / iron-sulfur cluster binding / host cell cytoplasm / symbiont entry into host cell / membrane
Similarity search - Function
Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein ...Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein / Bacteriophage lambda tail assembly protein I / : / : / Tip attachment protein J,FNIII-A domain / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Tip attachment protein J / Putative phage tail protein / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Putative tail fiber protein / Putative minor tail protein / Putative tail assembly protein / Putative minor tail protein / Tape measure protein
Similarity search - Component
Biological speciesEscherichia phage T1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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: Viruses / Year: 2025
Title: The In Situ Structure of T-Series T1 Reveals a Conserved Lambda-Like Tail Tip.
Authors: Yuan Chen / Hao Xiao / Junquan Zhou / Zeng Peng / Yuning Peng / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of ...It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of siphophages remain scarce. Using cryo-EM, we resolved the structures of T-series siphophage T1, encompassing its head, connector complex, tail tube, and tail tip, at near-atomic resolution. The density maps enabled us to build the atomic models for the majority of T1 proteins. The T1 head comprises 415 copies of the major capsid protein gp47, arranged into an icosahedron with a triangulation number of seven, decorated with 80 homologous trimers and 60 heterotrimers along the threefold and quasi-threefold axes of the icosahedron. The T1 connector complex is composed of two dodecamers (a portal and an adaptor) and two hexamers (a stopper and a tail terminator). The flexible tail tube comprises approximately 34 hexameric rings of tail tube. The extensive disulfide bond network along the successive tail rings may mediate the flexible bending. The distal tip of T1, which is cone-shaped and assembled by proteins gp33, gp34, gp36, gp37, and gp38, displays structural similarity to that of phage lambda. In conjunction with previous studies of lambda-like siphophages, our structure will facilitate further exploration of the structural and mechanistic aspects of lambda-like siphophages.
History
DepositionDec 30, 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
Revision 1.1Sep 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: Putative tail fiber protein
A: Putative tail assembly protein
J: Putative minor tail protein
H: Putative minor tail protein
B: Tape measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,3696
Polymers297,0185
Non-polymers3521
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Putative tail ... , 2 types, 2 molecules SA

#1: Protein Putative tail fiber protein


Mass: 130265.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: A0A3S9W0W9
#2: Protein Putative tail assembly protein


Mass: 20916.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: Q6XQC0

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Putative minor tail ... , 2 types, 2 molecules JH

#3: Protein Putative minor tail protein


Mass: 29058.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: A0A3S9W0Y3
#4: Protein Putative minor tail protein


Mass: 12992.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: Q6XQC3

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Protein / Non-polymers , 2 types, 2 molecules B

#5: Protein Tape measure protein / TMP / Gene product 38 / gp38


Mass: 103784.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T1 (virus) / References: UniProt: Q6XQC4
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: #1-#5 / 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4467 / Symmetry type: POINT
RefinementHighest resolution: 4.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410230
ELECTRON MICROSCOPYf_angle_d0.72313877
ELECTRON MICROSCOPYf_dihedral_angle_d5.2421393
ELECTRON MICROSCOPYf_chiral_restr0.0481505
ELECTRON MICROSCOPYf_plane_restr0.0061822

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