9LW8 | pdb_00009lw8

Bottom cap of bacteriophage Mycofy1 mature head (C5 symmetry)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 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

Cryo-EM Reveals Structural Diversity in Prolate-headed Mycobacteriophage Mycofy1.

Li, X.Shao, Q.Li, L.Xie, L.Ruan, Z.Fang, Q.

(2025) J Mol Biology 437: 169126-169126

  • DOI: https://doi.org/10.1016/j.jmb.2025.169126
  • Primary Citation of Related Structures:  
    9LW6, 9LW7, 9LW8, 9LW9, 9LWA

  • PubMed Abstract: 

    Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that Mycofy1 possesses a prolate head and a long non-contractile tail. We determined structures of its head, head-to-tail interface, terminator, and tail tube to resolutions of ∼3.5 Å. Unexpectedly, we identified two distinct types of prolate head structures, exhibiting a 36-degree relative rotation in the top cap region. Additionally, the head-to-tail interface demonstrated flexibility. Our structures provide the first high-resolution cryo-EM data of a mycobacteriophage with a prolate head, as well as detailed structural information of the head-to-tail interface and head-proximal tail region in this phage group. These findings advance our understanding of assembly mechanisms in tailed bacteriophages.


  • Organizational Affiliation
    • School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage capsid-like C-terminal domain-containing protein543Mycolicibacterium phage Mycofy1Mutation(s): 0 
UniProt
Find proteins for Q854Z2 (Mycobacterium phage Che9c)
Explore Q854Z2 
Go to UniProtKB:  Q854Z2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ854Z2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Shenzhen Science and Technology ProgramChinaJCYJ20240813180500001
Shenzhen Science and Technology ProgramChinaZDSYS20230626091203007

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references