5KCS

Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Evernimycin, mRNA, TetM and P-site tRNA at 3.9A resolution


Experimental Data Snapshot

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

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This is version 2.1 of the entry. See complete history


Literature

Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome.

Arenz, S.Juette, M.F.Graf, M.Nguyen, F.Huter, P.Polikanov, Y.S.Blanchard, S.C.Wilson, D.N.

(2016) Proc Natl Acad Sci U S A 113: 7527-7532

  • DOI: https://doi.org/10.1073/pnas.1604790113
  • Primary Citation of Related Structures:  
    5KCR, 5KCS

  • PubMed Abstract: 

    The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.


  • Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany;


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth 1D]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth 1E]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth 1F]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth 1G]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth 1H]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12H [auth 1L]121Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth 1I]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10J [auth 1J]165Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11K [auth 1K]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13L [auth 1N]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14M [auth 1O]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15N [auth 1P]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16O [auth 1Q]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17P [auth 1R]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Q [auth 1S]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19R [auth 1T]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20S [auth 1U]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21T [auth 1V]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22U [auth 1W]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23V [auth 1X]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24W [auth 1Y]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25X [auth 1Z]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Y [auth 10]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Z [auth 11]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AA [auth 12]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BA [auth 13]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31CA [auth 14]70Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth 15]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth 16]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FA [auth 17]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth 18]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HA [auth 19]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2JA [auth 1b]241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3KA [auth 1c]233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4LA [auth 1d]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5MA [auth 1e]167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6NA [auth 1f]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7OA [auth 1g]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8PA [auth 1h]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9QA [auth 1i]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10RA [auth 1j]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11SA [auth 1k]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12TA [auth 1l]124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13UA [auth 1m]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14VA [auth 1n]101Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15WA [auth 1o]89Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16XA [auth 1p]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17YA [auth 1q]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18ZA [auth 1r]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AB [auth 1s]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BB [auth 1t]87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21CB [auth 1u]71Escherichia coli K-12Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Tetracycline resistance protein TetM from transposon Tn916EB [auth 1w]639Enterococcus faecalisMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S Ribosomal RNAA [auth 1A]2,904Escherichia coli K-12
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S Ribosomal RNAB [auth 1B]120Escherichia coli K-12
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Entity ID: 35
MoleculeChains LengthOrganismImage
16S Ribosomal RNAIA [auth 1a]1,539Escherichia coli K-12
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Entity ID: 56
MoleculeChains LengthOrganismImage
mRNADB [auth 1v]60synthetic construct
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Entity ID: 58
MoleculeChains LengthOrganismImage
P-site tRNAFB [auth 1x]77Escherichia coli K-12
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVN
Query on EVN

Download Ideal Coordinates CCD File 
GB [auth 1A](2R,3R,4R,6S)-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7S,7aR)-6-{[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5S,6S)-6-({(2R,3aS,3a'R,6S,7R,7' R,7aS,7a'S)-7'-[(2,4-dihydroxy-6-methylbenzoyl)oxy]-7-hydroxyoctahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}ox y)-4-hydroxy-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-3-hydroxy-5-methoxy-6-methyltetrahydro-2H-pyran-4- yl]oxy}-4',7-dihydroxy-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-4-{[(2R,4S,5R, 6S)-5-methoxy-4,6-dimethyl-4-nitrotetrahydro-2H-pyran-2-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name)
C70 H97 Cl2 N O38
UPADRKHAIMTUCC-LRNXXXSBSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Illinois State Startup FundsUnited States--
German Research Foundation (DFG)GermanyFOR1805
German Research Foundation (DFG)GermanyWI3285/3-2
German Research Foundation (DFG)GermanyGRK1721
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM079238
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098859

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2018-07-18
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2019-12-25
    Changes: Author supporting evidence