6WYV

E. coli 50S ribosome bound to compounds 47 and VS1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 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

Synthetic group A streptogramin antibiotics that overcome Vat resistance.

Li, Q.Pellegrino, J.Lee, D.J.Tran, A.A.Chaires, H.A.Wang, R.Park, J.E.Ji, K.Chow, D.Zhang, N.Brilot, A.F.Biel, J.T.van Zundert, G.Borrelli, K.Shinabarger, D.Wolfe, C.Murray, B.Jacobson, M.P.Muhle, E.Chesneau, O.Fraser, J.S.Seiple, I.B.

(2020) Nature 586: 145-150

  • DOI: 10.1038/s41586-020-2761-3
  • Primary Citation of Related Structures:  
    6WYV, 6PCH, 6PC6, 6PC5, 6PC8, 6PC7, 6PCR, 6PCQ, 6PCT, 6PCS

  • PubMed Abstract: 
  • Natural products serve as chemical blueprints for most antibiotics in clinical use. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of a ...

    Natural products serve as chemical blueprints for most antibiotics in clinical use. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class of antibiotics 1 . Virginiamycin acetyltransferase (Vat) enzymes are resistance proteins that provide protection against streptogramins 2 , potent antibiotics against Gram-positive bacteria that inhibit the bacterial ribosome 3 . Owing to the challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of group A streptogramins, analogues that overcome the resistance conferred by Vat enzymes have not been previously developed 2 . Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics with extensive structural variability. Using cryo-electron microscopy and forcefield-based refinement, we characterize the binding of eight analogues to the bacterial ribosome at high resolution, revealing binding interactions that extend into the peptidyl tRNA-binding site and towards synergistic binders that occupy the nascent peptide exit tunnel. One of these analogues has excellent activity against several streptogramin-resistant strains of Staphylococcus aureus, exhibits decreased rates of acetylation in vitro, and is effective at lowering bacterial load in a mouse model of infection. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA. ian.seiple@ucsf.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2K271Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Go to UniProtKB:  P60422
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15L144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Go to UniProtKB:  P02413
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4M201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Go to UniProtKB:  P60723
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3N209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Go to UniProtKB:  P60438
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13O142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AA10
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
VIRGINIAMYCIN S1C7Streptomyces virginiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAI2904Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAJ118Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O7S
Query on O7S

Download CCD File 
I
(3R,4R,5E,10E,12E,14S,16R,26aR)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione
C30 H40 F N3 O6
GWIAEMBAGQHJHW-CLECSTCYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEA
Query on MEA
CL-PEPTIDE LINKINGC10 H13 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 8
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000227
Query on PRD_000227
CVIRGINIAMYCIN S1Cyclic peptide /  Antibiotic, Antimicrobial

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM123159
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124149

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-10-07
    Changes: Database references