9L9P | pdb_00009l9p

Cryo-EM structure of bacteriophage T1 tail tip complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The In Situ Structure of T-Series T1 Reveals a Conserved Lambda-Like Tail Tip.

Chen, Y.Xiao, H.Zhou, J.Peng, Z.Peng, Y.Song, J.Zheng, J.Liu, H.

(2025) Viruses 17

  • DOI: https://doi.org/10.3390/v17030351
  • Primary Citation of Related Structures:  
    9KZJ, 9L01, 9L0E, 9L0F, 9L9P

  • PubMed 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 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.


  • Organizational Affiliation
    • Key Laboratory for Matter Microstructure and Function of Hunan Province, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tail fiber proteinA [auth S]1,172Escherichia phage T1Mutation(s): 0 
UniProt
Find proteins for Q6XQB9 (Escherichia phage T1)
Explore Q6XQB9 
Go to UniProtKB:  Q6XQB9
Entity Groups  
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UniProt GroupQ6XQB9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tail assembly proteinB [auth A]199Escherichia phage T1Mutation(s): 0 
UniProt
Find proteins for Q6XQC0 (Escherichia phage T1)
Explore Q6XQC0 
Go to UniProtKB:  Q6XQC0
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XQC0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative minor tail proteinC [auth J]260Escherichia phage T1Mutation(s): 0 
UniProt
Find proteins for Q6XQC2 (Escherichia phage T1)
Explore Q6XQC2 
Go to UniProtKB:  Q6XQC2
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UniProt GroupQ6XQC2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative minor tail proteinD [auth H]117Escherichia phage T1Mutation(s): 0 
UniProt
Find proteins for Q6XQC3 (Escherichia phage T1)
Explore Q6XQC3 
Go to UniProtKB:  Q6XQC3
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UniProt GroupQ6XQC3
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tape measure proteinE [auth B]957Escherichia phage T1Mutation(s): 0 
UniProt
Find proteins for Q6XQC4 (Escherichia phage T1)
Explore Q6XQC4 
Go to UniProtKB:  Q6XQC4
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UniProt GroupQ6XQC4
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
F [auth J]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China12034006
National Natural Science Foundation of China (NSFC)China32430020
National Natural Science Foundation of China (NSFC)China32071209

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references