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 6U5B | pdb_00006u5b

CryoEM Structure of Pyocin R2 - precontracted - baseplate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 1,518.43 kDa 
  • Atom Count: 103,392 
  • Modeled Residue Count: 13,608 
  • Deposited Residue Count: 14,034 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tri1a PA0618295Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XCX5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XCX5 
Go to UniProtKB:  G3XCX5
Entity Groups
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UniProt GroupG3XCX5
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Reference Sequence
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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
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UniProt GroupG3XD39
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tube PA0623167Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for Q9I5S9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I5S9 
Go to UniProtKB:  Q9I5S9
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UniProt GroupQ9I5S9
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tri2 PA0619177Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XD92 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD92 
Go to UniProtKB:  G3XD92
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UniProt GroupG3XD92
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Sheath Initiator PA0617108Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XD42 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD42 
Go to UniProtKB:  G3XD42
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UniProt GroupG3XD42
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Glue PA062768Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XD62 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
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Go to UniProtKB:  G3XD62
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UniProt GroupG3XD62
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Ripcord PA0626290Pseudomonas aeruginosa PAO1Mutation(s): 0 
UniProt
Find proteins for G3XD65 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD65 
Go to UniProtKB:  G3XD65
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UniProt GroupG3XD65
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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

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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