6U5J

CryoEM Structure of Pyocin R2 - postcontracted - collar


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Action of a minimal contractile bactericidal nanomachine.

Ge, P.Scholl, D.Prokhorov, N.S.Avaylon, J.Shneider, M.M.Browning, C.Buth, S.A.Plattner, M.Chakraborty, U.Ding, K.Leiman, P.G.Miller, J.F.Zhou, Z.H.

(2020) Nature 580: 658-662

  • DOI: https://doi.org/10.1038/s41586-020-2186-z
  • Primary Citation of Related Structures:  
    5CES, 6PYT, 6U5B, 6U5F, 6U5H, 6U5J, 6U5K

  • PubMed Abstract: 

    R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics 1-4 . Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold 1,2 . Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage 5 . Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.


  • 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
Collar PA0615171Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XD82 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD82 
Go to UniProtKB:  G3XD82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD82
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sheath PA0622386Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XD39 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD39 
Go to UniProtKB:  G3XD39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD39
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONRELION1.4

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 StatesR01GM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI085318
Swiss National Science FoundationSwitzerland31003A_146284
National Science Foundation (NSF, United States)United StatesXSEDE MCB140140

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references