7UW1

A. baumannii 70S ribosome-Streptothricin-D complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.21 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

Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome.

Morgan, C.E.Kang, Y.S.Green, A.B.Smith, K.P.Dowgiallo, M.G.Miller, B.C.Chiaraviglio, L.Truelson, K.A.Zulauf, K.E.Rodriguez, S.Kang, A.D.Manetsch, R.Yu, E.W.Kirby, J.E.

(2023) PLoS Biol 21: e3002091-e3002091

  • DOI: https://doi.org/10.1371/journal.pbio.3002091
  • Primary Citation of Related Structures:  
    7UVV, 7UVW, 7UVX, 7UVY, 7UVZ, 7UW1

  • PubMed Abstract: 

    The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we establish the activity spectrum of nourseothricin and its main components, streptothricin F (S-F, 1 lysine) and streptothricin D (S-D, 3 lysines), purified to homogeneity, against highly drug-resistant, carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii. For CRE, the MIC50 and MIC90 for S-F and S-D were 2 and 4 μM, and 0.25 and 0.5 μM, respectively. S-F and nourseothricin showed rapid, bactericidal activity. S-F and S-D both showed approximately 40-fold greater selectivity for prokaryotic than eukaryotic ribosomes in in vitro translation assays. In vivo, delayed renal toxicity occurred at >10-fold higher doses of S-F compared with S-D. Substantial treatment effect of S-F in the murine thigh model was observed against the otherwise pandrug-resistant, NDM-1-expressing Klebsiella pneumoniae Nevada strain with minimal or no toxicity. Cryo-EM characterization of S-F bound to the A. baumannii 70S ribosome defines extensive hydrogen bonding of the S-F steptolidine moiety, as a guanine mimetic, to the 16S rRNA C1054 nucleobase (Escherichia coli numbering) in helix 34, and the carbamoylated gulosamine moiety of S-F with A1196, explaining the high-level resistance conferred by corresponding mutations at the residues identified in single rrn operon E. coli. Structural analysis suggests that S-F probes the A-decoding site, which potentially may account for its miscoding activity. Based on unique and promising activity, we suggest that the streptothricin scaffold deserves further preclinical exploration as a potential therapeutic for drug-resistant, gram-negative pathogens.


  • Organizational Affiliation

    Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 0]51Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 1]44Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35C [auth 2]64Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 3]38Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2G [auth C]274Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3H [auth D]212Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4I [auth E]200Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5J [auth F]178Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6K [auth G]177Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9L [auth H]148Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13M [auth I]142Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth J]122Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15O [auth K]146Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16P [auth L]137Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17Q [auth M]125Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18R [auth N]116Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19S [auth O]122Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20T [auth P]119Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21U [auth Q]103Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22V [auth R]109Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23W [auth S]106Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24X [auth T]105Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Y [auth U]98Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Z [auth V]85Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28AA [auth W]78Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BA [auth X]65Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CA [auth Y]58Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth Z]61Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2FA [auth b]250Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3GA [auth c]250Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4HA [auth d]208Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5IA [auth e]165Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6JA [auth f]127Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7KA [auth g]156Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth h]131Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9MA [auth i]128Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10NA [auth j]103Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11OA [auth k]128Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth l]124Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth m]118Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14RA [auth n]101Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth o]89Acinetobacter baumannii AB0057Mutation(s): 0 
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UniProt GroupB7I3U0
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth p]101Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for A0A1V3DIZ9 (Acinetobacter baumannii)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth q]85Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for B7IA30 (Acinetobacter baumannii (strain AB0057))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth r]75Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for A0A372MP10 (Acinetobacter haemolyticus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth s]91Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for B7IA35 (Acinetobacter baumannii (strain AB0057))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth t]88Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for B7I5N9 (Acinetobacter baumannii (strain AB0057))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21YA [auth u]71Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for A0A0Q7FMS9 (Acinetobacter sp. Root1280)
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Entity ID: 5
MoleculeChains LengthOrganismImage
23s ribosomal RNAE [auth A]2,918Acinetobacter baumannii AB0057
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Entity ID: 6
MoleculeChains LengthOrganismImage
5s ribosomal RNAF [auth B]115Acinetobacter baumannii AB0057
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Entity ID: 31
MoleculeChains LengthOrganismImage
16s Ribosomal RNAEA [auth a]1,544Acinetobacter baumannii AB0057
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OIY (Subject of Investigation/LOI)
Query on OIY

Download Ideal Coordinates CCD File 
AB [auth A]
BB [auth A]
CB [auth A]
DB [auth A]
EB [auth A]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
IB [auth W],
JB [auth a],
KB [auth a],
LB [auth a],
MB [auth a]
Streptothricin D
C31 H58 N12 O10
WUJTXMVGXDQPNN-OTQKCRDJSA-N
ZN
Query on ZN

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ZA [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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HB [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4080:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references