8UVR image
Entry Detail
PDB ID:
8UVR
Title:
Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with spectinomycin, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.60A resolution
Biological Source:
PDB Version:
Deposition Date:
2023-11-03
Release Date:
2024-08-07
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:V (auth: 10), ZB (auth: 20)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:W (auth: 11), AC (auth: 21)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:X (auth: 12), BC (auth: 22)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:Y (auth: 13), CC (auth: 23)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:Z (auth: 14), DC (auth: 24)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:AA (auth: 15), EC (auth: 25)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:BA (auth: 16), FC (auth: 26)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:CA (auth: 17), GC (auth: 27)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:DA (auth: 18), HC (auth: 28)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:EA (auth: 19), IC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:23S Ribosomal RNA
Chain IDs:A (auth: 1A), EB (auth: 2A)
Chain Length:1521
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:5S Ribosomal RNA
Chain IDs:B (auth: 1B), FB (auth: 2B)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:C (auth: 1D), GB (auth: 2D)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:D (auth: 1E), HB (auth: 2E)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:E (auth: 1F), IB (auth: 2F)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:F (auth: 1G), JB (auth: 2G)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:G (auth: 1H), KB (auth: 2H)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:H (auth: 1I), LB (auth: 2I)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:I (auth: 1N), MB (auth: 2N)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:J (auth: 1O), NB (auth: 2O)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:K (auth: 1P), OB (auth: 2P)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:L (auth: 1Q), PB (auth: 2Q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:M (auth: 1R), QB (auth: 2R)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:N (auth: 1S), RB (auth: 2S)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:O (auth: 1T), SB (auth: 2T)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:P (auth: 1U), TB (auth: 2U)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:Q (auth: 1V), UB (auth: 2V)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:R (auth: 1W), VB (auth: 2W)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:S (auth: 1X), WB (auth: 2X)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:T (auth: 1Y), XB (auth: 2Y)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:U (auth: 1Z), YB (auth: 2Z)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:16S Ribosomal RNA
Chain IDs:FA (auth: 1a), JC (auth: 2a)
Chain Length:1521
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:GA (auth: 1b), KC (auth: 2b)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:HA (auth: 1c), LC (auth: 2c)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:IA (auth: 1d), MC (auth: 2d)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:JA (auth: 1e), NC (auth: 2e)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:KA (auth: 1f), OC (auth: 2f)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:LA (auth: 1g), PC (auth: 2g)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:MA (auth: 1h), QC (auth: 2h)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:NA (auth: 1i), RC (auth: 2i)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:OA (auth: 1j), SC (auth: 2j)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:PA (auth: 1k), TC (auth: 2k)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:QA (auth: 1l), UC (auth: 2l)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:RA (auth: 1m), VC (auth: 2m)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14 type Z
Chain IDs:SA (auth: 1n), WC (auth: 2n)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:TA (auth: 1o), XC (auth: 2o)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:UA (auth: 1p), YC (auth: 2p)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:VA (auth: 1q), ZC (auth: 2q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:WA (auth: 1r), AD (auth: 2r)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:XA (auth: 1s), BD (auth: 2s)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:YA (auth: 1t), CD (auth: 2t)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein Thx
Chain IDs:ZA (auth: 1u), DD (auth: 2u)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:MF-mRNA
Chain IDs:AB (auth: 1v), ED (auth: 2v)
Chain Length:24
Number of Molecules:2
Biological Source:Escherichia phage T4
Polymer Type:polyribonucleotide
Description:A-site and E-site Deacylated tRNAphe
Chain IDs:BB (auth: 1w), DB (auth: 1y), FD (auth: 2w), HD (auth: 2y)
Chain Length:113
Number of Molecules:4
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:P-site Deacylated tRNAmet
Chain IDs:CB (auth: 1x), GD (auth: 2x)
Chain Length:96
Number of Molecules:2
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD QA ASP modified residue
2MA A A modified residue
2MG FA G modified residue
4OC FA C modified residue
4SU BB U modified residue
5MC A C modified residue
5MU A U modified residue
G7M FA G modified residue
M2G FA G modified residue
MA6 FA A modified residue
MIA BB A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
UR3 FA U modified residue
Primary Citation
Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus.
Proc.Natl.Acad.Sci.USA 121 e2314101120 e2314101120 (2024)
PMID: 38165935 DOI: 10.1073/pnas.2314101120

Abstact

Mycobacterium abscessus (Mab), a nontuberculous mycobacterial (NTM) species, is an emerging pathogen with high intrinsic drug resistance. Current standard-of-care therapy results in poor outcomes, demonstrating the urgent need to develop effective antimycobacterial regimens. Through synthetic modification of spectinomycin (SPC), we have identified a distinct structural subclass of N-ethylene linked aminomethyl SPCs (eAmSPCs) that are up to 64-fold more potent against Mab over the parent SPC. Mechanism of action and crystallography studies demonstrate that the eAmSPCs display a mode of ribosomal inhibition consistent with SPC. However, they exert their increased antimicrobial activity through enhanced accumulation, largely by circumventing efflux mechanisms. The N-ethylene linkage within this series plays a critical role in avoiding TetV-mediated efflux, as lead eAmSPC 2593 displays a mere fourfold susceptibility improvement against Mab ΔtetV, in contrast to the 64-fold increase for SPC. Even a minor shortening of the linkage by a single carbon, akin to 1st generation AmSPC 1950, results in a substantial increase in MICs and a 16-fold rise in susceptibility against Mab ΔtetV. These shifts suggest that longer linkages might modify the kinetics of drug expulsion by TetV, ultimately shifting the equilibrium towards heightened intracellular concentrations and enhanced antimicrobial efficacy. Furthermore, lead eAmSPCs were also shown to synergize with various classes of anti-Mab antibiotics and retain activity against clinical isolates and other mycobacterial strains. Encouraging pharmacokinetic profiles coupled with robust efficacy in Mab murine infection models suggest that eAmSPCs hold the potential to be developed into treatments for Mab and other NTM infections.

Legend

Protein

Chemical

Disease

Primary Citation of related structures