7RYF image
Deposition Date 2021-08-25
Release Date 2022-02-02
Last Version Date 2025-03-19
Entry Detail
PDB ID:
7RYF
Keywords:
Title:
A. baumannii Ribosome-TP-6076 complex: P-site tRNA 70S
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.65 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:A (auth: 0)
Chain Length:51
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule: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)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:C (auth: 2)
Chain Length:64
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:E (auth: A)
Chain Length:1544
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:F (auth: B)
Chain Length:250
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:G (auth: C)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:H (auth: D)
Chain Length:212
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:I (auth: E)
Chain Length:200
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:J (auth: F)
Chain Length:178
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:K (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:L (auth: H)
Chain Length:148
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:M (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:N (auth: J)
Chain Length:103
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:O (auth: K)
Chain Length:128
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:P (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:Q (auth: M)
Chain Length:118
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:R (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:S (auth: O)
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:T (auth: P)
Chain Length:101
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:U (auth: Q)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:V (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:W (auth: S)
Chain Length:106
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:X (auth: T)
Chain Length:88
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:Y (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: V)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule: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)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:BA (auth: X)
Chain Length:65
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule: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)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:DA (auth: Z)
Chain Length:61
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:EA (auth: a)
Chain Length:1544
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:FA (auth: b)
Chain Length:250
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: c)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: d)
Chain Length:212
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: e)
Chain Length:200
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: f)
Chain Length:178
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: g)
Chain Length:156
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: h)
Chain Length:148
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: i)
Chain Length:128
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:NA (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: k)
Chain Length:128
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:PA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:RA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: o)
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: p)
Chain Length:101
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: q)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule: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)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: s)
Chain Length:106
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: t)
Chain Length:88
Number of Molecules:1
Biological Source:Acinetobacter baumannii (strain AB0057)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:YA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Molecule:tRNA-met
Chain IDs:ZA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii AB0057
Polymer Type:polyribonucleotide
Molecule: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
An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii.
Mbio 13 e0373221 e0373221 (2022)
PMID: 35100868 DOI: 10.1128/mbio.03732-21

Abstact

Antibiotic resistance among bacterial pathogens continues to pose a serious global health threat. Multidrug-resistant (MDR) strains of the Gram-negative organism Acinetobacter baumannii utilize a number of resistance determinants to evade current antibiotics. One of the major resistance mechanisms employed by these pathogens is the use of multidrug efflux pumps. These pumps extrude xenobiotics directly out of bacterial cells, resulting in treatment failures when common antibiotics are administered. Here, the structure of the novel tetracycline antibiotic TP-6076, bound to both the Acinetobacter drug efflux pump AdeJ and the ribosome from Acinetobacter baumannii, using single-particle cryo-electron microscopy (cryo-EM), is elucidated. In this work, the structure of the AdeJ-TP-6076 complex is solved, and we show that AdeJ utilizes a network of hydrophobic interactions to recognize this fluorocycline. Concomitant with this, we elucidate three structures of TP-6076 bound to the A. baumannii ribosome and determine that its binding is stabilized largely by electrostatic interactions. We then compare the differences in binding modes between TP-6076 and the related tetracycline antibiotic eravacycline in both targets. These differences suggest that modifications to the tetracycline core may be able to alter AdeJ binding while maintaining interactions with the ribosome. Together, this work highlights how different mechanisms are used to stabilize the binding of tetracycline-based compounds to unique bacterial targets and provides guidance for the future clinical development of tetracycline antibiotics. IMPORTANCE Treatment of antibiotic-resistant organisms such as A. baumannii represents an ongoing issue for modern medicine. The multidrug efflux pump AdeJ serves as a major resistance determinant in A. baumannii through its action of extruding antibiotics from the cell. In this work, we use cryo-EM to show how AdeJ recognizes the experimental tetracycline antibiotic TP-6076 and prevents this drug from interacting with the A. baumannii ribosome. Since AdeJ and the ribosome use different binding modes to stabilize interactions with TP-6076, exploiting these differences may guide future drug development for combating antibiotic-resistant A. baumannii and potentially other strains of MDR bacteria.

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Primary Citation of related structures