8G01

YES Complex - E. coli MraY, Protein E ID21, E. coli SlyD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

The mechanism of the phage-encoded protein antibiotic from Phi X174.

Orta, A.K.Riera, N.Li, Y.E.Tanaka, S.Yun, H.G.Klaic, L.Clemons Jr., W.M.

(2023) Science 381: eadg9091-eadg9091

  • DOI: https://doi.org/10.1126/science.adg9091
  • Primary Citation of Related Structures:  
    8G01, 8G02

  • PubMed Abstract: 

    The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that protein E bridges two bacterial proteins to form the transmembrane YES complex [MraY, protein E, sensitivity to lysis D (SlyD)]. Protein E inhibits peptidoglycan biosynthesis by obstructing the MraY active site leading to loss of lipid I production. We experimentally validate this result for two different viral species, providing a clear model for bacterial lysis and unifying previous experimental data. Additionally, we characterize the Escherichia coli MraY structure-revealing features of this essential enzyme-and the structure of the chaperone SlyD bound to a protein. Our structures provide insights into the mechanism of phage-mediated lysis and for structure-based design of phage therapeutics.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospho-N-acetylmuramoyl-pentapeptide-transferaseA,
D [auth E]
360Escherichia coli K-12Mutation(s): 0 
Gene Names: mraYmurXb0087JW0085
EC: 2.7.8.13
Membrane Entity: Yes 
UniProt
Find proteins for P0A6W3 (Escherichia coli (strain K12))
Explore P0A6W3 
Go to UniProtKB:  P0A6W3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6W3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GPEB,
C [auth G]
82Escherichia phage ID21Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q2LMB7 (Escherichia phage ID21)
Explore Q2LMB7 
Go to UniProtKB:  Q2LMB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2LMB7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FKBP-type peptidyl-prolyl cis-trans isomerase SlyDE [auth D],
F [auth C]
154Escherichia coli K-12Mutation(s): 0 
Gene Names: slyDb3349JW3311
EC: 5.2.1.8
UniProt
Find proteins for P0A9K9 (Escherichia coli (strain K12))
Explore P0A9K9 
Go to UniProtKB:  P0A9K9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9K9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.2.0+210817
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTISOLDE1.2.2

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 StatesGM114611
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM105385

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Refinement description