7SFS

In situ cryo-EM structure of bacteriophage Sf6 portal:gp7 complex at 2.7A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine.

Li, F.Hou, C.D.Yang, R.Whitehead III, R.Teschke, C.M.Cingolani, G.

(2022) Sci Adv 8: eadc9641-eadc9641

  • DOI: https://doi.org/10.1126/sciadv.adc9641
  • Primary Citation of Related Structures:  
    7SFS, 7SG7, 7SP4, 7SPU, 7UKJ

  • PubMed Abstract: 

    Sf6 is a bacterial virus that infects the human pathogen Shigella flexneri. Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gene 3 protein708Lederbergvirus Sf6Mutation(s): 0 
UniProt
Find proteins for Q716H2 (Shigella phage Sf6)
Explore Q716H2 
Go to UniProtKB:  Q716H2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ716H2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gene 7 protein160Lederbergvirus Sf6Mutation(s): 0 
UniProt
Find proteins for Q716G8 (Shigella phage Sf6)
Explore Q716G8 
Go to UniProtKB:  Q716G8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ716G8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140733

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Data collection