8V40

CryoEM Structure of Diffocin - postcontracted - Collar - final state

  • Classification: VIRUS LIKE PARTICLE
  • Organism(s): Clostridioides difficile
  • Expression System: Bacillus subtilis
  • Mutation(s): No 

  • Deposited: 2023-11-28 Released: 2024-08-28 
  • Deposition Author(s): Cai, X.Y., He, Y., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Atomic structures of a bacteriocin targeting Gram-positive bacteria.

Cai, X.He, Y.Yu, I.Imani, A.Scholl, D.Miller, J.F.Zhou, Z.H.

(2024) Nat Commun 15: 7057-7057

  • DOI: https://doi.org/10.1038/s41467-024-51038-w
  • Primary Citation of Related Structures:  
    8V3T, 8V3W, 8V3X, 8V3Y, 8V3Z, 8V40, 8V41, 8V43

  • PubMed Abstract: 

    Due to envelope differences between Gram-positive and Gram-negative bacteria, engineering precision bactericidal contractile nanomachines requires atomic-level understanding of their structures; however, only those killing Gram-negative bacteria are currently known. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with target envelope differences. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.


  • Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tube (CD1364)142Clostridioides difficileMutation(s): 0 
Gene Names: xkdM
UniProt
Find proteins for A0A031WFC4 (Clostridioides difficile)
Explore A0A031WFC4 
Go to UniProtKB:  A0A031WFC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A031WFC4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sheath (CD1363)354Clostridioides difficileMutation(s): 0 
Gene Names: SAMEA3375112_00264
UniProt
Find proteins for A0A9Q7ZU73 (Clostridioides difficile)
Explore A0A9Q7ZU73 
Go to UniProtKB:  A0A9Q7ZU73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9Q7ZU73
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Collar (CD1362)147Clostridioides difficileMutation(s): 0 
Gene Names: rtbA
UniProt
Find proteins for A0A1X9JZ99 (Clostridioides difficile)
Explore A0A1X9JZ99 
Go to UniProtKB:  A0A1X9JZ99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1X9JZ99
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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 StatesGM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI085318

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release