7UVV image
Entry Detail
PDB ID:
7UVV
EMDB ID:
Keywords:
Title:
A. baumannii ribosome-Streptothricin-F complex: 70S with P-site tRNA
Biological Source:
PDB Version:
Deposition Date:
2022-05-02
Release Date:
2023-04-19
Method Details:
Experimental Method:
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:A (auth: 0)
Chain Length:51
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:B (auth: 1)
Chain Length:44
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:C (auth: 2)
Chain Length:64
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Description:23s ribosomal RNA
Chain IDs:E (auth: A)
Chain Length:1544
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Description:5s ribosomal RNA
Chain IDs:F (auth: B)
Chain Length:115
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:G (auth: C)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:H (auth: D)
Chain Length:208
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:I (auth: E)
Chain Length:165
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:J (auth: F)
Chain Length:178
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:K (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:L (auth: H)
Chain Length:148
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:M (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:N (auth: J)
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:O (auth: K)
Chain Length:128
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:P (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:Q (auth: M)
Chain Length:125
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:R (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:S (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:T (auth: P)
Chain Length:119
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:U (auth: Q)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:V (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:W (auth: S)
Chain Length:106
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:X (auth: T)
Chain Length:88
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:Y (auth: U)
Chain Length:98
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:Z (auth: V)
Chain Length:77
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:AA (auth: W)
Chain Length:78
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:BA (auth: X)
Chain Length:65
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:CA (auth: Y)
Chain Length:58
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:DA (auth: Z)
Chain Length:61
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Description:16s Ribosomal RNA
Chain IDs:EA (auth: a)
Chain Length:1544
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:FA (auth: b)
Chain Length:115
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:GA (auth: c)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:HA (auth: d)
Chain Length:208
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:IA (auth: e)
Chain Length:165
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:JA (auth: f)
Chain Length:178
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:KA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:LA (auth: h)
Chain Length:148
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:MA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:NA (auth: j)
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:OA (auth: k)
Chain Length:128
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:PA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:QA (auth: m)
Chain Length:125
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:RA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:SA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:TA (auth: p)
Chain Length:119
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:UA (auth: q)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:VA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:WA (auth: s)
Chain Length:106
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:XA (auth: t)
Chain Length:88
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:YA (auth: u)
Chain Length:98
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Description:tRNA-met
Chain IDs:ZA (auth: v)
Chain Length:77
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:AB (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG EA G modified residue
4OC EA C modified residue
4SU ZA U modified residue
5MC EA C modified residue
5MU ZA U modified residue
7MG EA G modified residue
H2U ZA U modified residue
MA6 EA A modified residue
PSU EA U modified residue
UR3 EA U modified residue
Primary Citation
Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome.
Plos Biol. 21 e3002091 e3002091 (2023)
PMID: 37192172 DOI: 10.1371/journal.pbio.3002091

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures