7JQL image
Deposition Date 2020-08-11
Release Date 2020-08-26
Last Version Date 2025-03-19
Entry Detail
PDB ID:
7JQL
Keywords:
Title:
Crystal structure of the Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A resolution
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: 10), YB (auth: 20)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: 11), ZB (auth: 21)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: 12), AC (auth: 22)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: 13), BC (auth: 23)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: 14), CC (auth: 24)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 15), DC (auth: 25)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 16), EC (auth: 26)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 17), FC (auth: 27)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 18), GC (auth: 28)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 19), HC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:A (auth: 1A), DB (auth: 2A)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:B (auth: 1B), EB (auth: 2B)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: 1D), FB (auth: 2D)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: 1E), GB (auth: 2E)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: 1F), HB (auth: 2F)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: 1G), IB (auth: 2G)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: 1H), JB (auth: 2H)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: 1I), KB (auth: 2I)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: 1N), LB (auth: 2N)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: 1O), MB (auth: 2O)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: 1P), NB (auth: 2P)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: 1Q), OB (auth: 2Q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: 1R), PB (auth: 2R)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: 1S), QB (auth: 2S)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: 1T), RB (auth: 2T)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: 1U), SB (auth: 2U)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: 1V), TB (auth: 2V)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: 1W), UB (auth: 2W)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: 1X), VB (auth: 2X)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: 1Y), WB (auth: 2Y)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: 1Z), XB (auth: 2Z)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:FA (auth: 1a), IC (auth: 2a)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:GA (auth: 1b), JC (auth: 2b)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:HA (auth: 1c), KC (auth: 2c)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:IA (auth: 1d), LC (auth: 2d)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:JA (auth: 1e), MC (auth: 2e)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:KA (auth: 1f), NC (auth: 2f)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:LA (auth: 1g), OC (auth: 2g)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:MA (auth: 1h), PC (auth: 2h)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:NA (auth: 1i), QC (auth: 2i)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:OA (auth: 1j), RC (auth: 2j)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:PA (auth: 1k), SC (auth: 2k)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:QA (auth: 1l), TC (auth: 2l)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:RA (auth: 1m), UC (auth: 2m)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:SA (auth: 1n), VC (auth: 2n)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:TA (auth: 1o), WC (auth: 2o)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:UA (auth: 1p), XC (auth: 2p)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:VA (auth: 1q), YC (auth: 2q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:WA (auth: 1r), ZC (auth: 2r)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:XA (auth: 1s), AD (auth: 2s)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:YA (auth: 1t), BD (auth: 2t)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:ZA (auth: 1u), CD (auth: 2u)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:AB (auth: 1v), DD (auth: 2v)
Chain Length:101
Number of Molecules:2
Biological Source:Escherichia virus T4
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:BB (auth: 1x), ED (auth: 2x)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Bac7-001
Chain IDs:CB (auth: 1z), FD (auth: 2z)
Chain Length:206
Number of Molecules:2
Biological Source:Bos taurus
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
2MU A U modified residue
4OC A C modified residue
4SU BB U modified residue
5MC A C modified residue
5MU A U modified residue
7MG FA G modified residue
M2G FA G modified residue
MA6 FA A modified residue
OMG A G modified residue
PSU A U modified residue
UR3 FA U modified residue
Primary Citation
Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens.
J.Med.Chem. 63 9590 9602 (2020)
PMID: 32787108 DOI: 10.1021/acs.jmedchem.0c00665

Abstact

Proline-rich antimicrobial peptides (PrAMPs) are promising lead compounds for developing new antimicrobials; however, their narrow spectrum of action is limiting. PrAMPs kill bacteria binding to their ribosomes and inhibiting protein synthesis. In this study, 133 derivatives of the PrAMP Bac7(1-16) were synthesized to identify the crucial residues for ribosome inactivation and antimicrobial activity. Then, five new Bac7(1-16) derivatives were conceived and characterized by antibacterial and membrane permeabilization assays, X-ray crystallography, and molecular dynamics simulations. Some derivatives displayed broad spectrum activity, encompassing Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus. Two peptides out of five acquired a weak membrane-perturbing activity while maintaining the ability to inhibit protein synthesis. These derivatives became independent of the SbmA transporter, commonly used by native PrAMPs, suggesting that they obtained a novel route to enter bacterial cells. PrAMP-derived compounds could become new-generation antimicrobials to combat antibiotic-resistant pathogens.

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Primary Citation of related structures