ISDA

Deposition Date 2020-10-16

Release Date 2022-01-19

Last Version Date 2024-05-29

Entry Detail

PDB ID:

7KGB

Keywords:

RIBOSOME/ANTIBIOTIC

Title:

CryoEM structure of A2296-methylated Mycobacterium tuberculosis ribosome bound with SEQ-9

Biological Source:

Source Organism:

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (Taxon ID: 83332)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.70 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:A (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH99 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 2
Gene (Uniprot):rpmG2
Chain IDs:B (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH95 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:C (auth: 2)
Chain Length:47
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH93 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:D (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH91 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:E (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH89 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:F (auth: 6)
Chain Length:80
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHA1 Pfam ID:PF01197

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:G (auth: A)
Chain Length:3138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:H (auth: B)
Chain Length:115
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:I (auth: C)
Chain Length:274
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHA5 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:J (auth: D)
Chain Length:201
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH87 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:K (auth: E)
Chain Length:223
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH85 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:L (auth: F)
Chain Length:96
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH83 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:M (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH81 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:N (auth: H)
Chain Length:132
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH79 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:O (auth: J)
Chain Length:101
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:A0A0T9D5H2 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:P (auth: K)
Chain Length:122
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHD9 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:Q (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHD7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:R (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHD5 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:S (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHD3 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:T (auth: O)
Chain Length:122
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHD1 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:U (auth: P)
Chain Length:113
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHC9 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:V (auth: Q)
Chain Length:135
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHC5 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:W (auth: R)
Chain Length:84
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHC3 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:X (auth: S)
Chain Length:93
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHC1 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:Y (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHB9 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:Z (auth: U)
Chain Length:105
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHB7 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:AA (auth: V)
Chain Length:215
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHB5 Pfam ID:PF01386, PF14693

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:BA (auth: W)
Chain Length:86
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHB3 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:CA (auth: X)
Chain Length:64
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P0DV54 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:DA (auth: Y)
Chain Length:77
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHA7 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:EA (auth: Z)
Chain Length:65
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WHA3 Pfam ID:PF00327

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:FA (auth: a)
Chain Length:3138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Protein Blast

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:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH37 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: d)
Chain Length:201
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH35 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: e)
Chain Length:223
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH33 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: f)
Chain Length:96
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH31 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH29 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: h)
Chain Length:132
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH27 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: i)
Chain Length:151
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH25 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: j)
Chain Length:101
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH67 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: k)
Chain Length:122
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH65 Pfam ID:PF00411

Protein Blast

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:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH63 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH61 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:RA (auth: n)
Chain Length:61
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH57 Pfam ID:PF00253

Protein Blast

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:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH55 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: p)
Chain Length:113
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH53 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: q)
Chain Length:135
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH51 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18 1
Gene (Uniprot):rpsR1
Chain IDs:VA (auth: r)
Chain Length:84
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH49 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: s)
Chain Length:93
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH45 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WH41 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37
Chain IDs:YA (auth: v)
Chain Length:215
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:A0A0U0UFA0

Polymer Type:polyribonucleotide
Molecule:tRNA-initiator Met(CAU)
Chain IDs:ZA (auth: y)
Chain Length:77
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Primary Citation

Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents.

Zhang, J, Lair, C, Roubert, C, Amaning, K, Barrio, M.B, Benedetti, Y, Cui, Z, Xing, Z, Li, X, Franzblau, S.G, Baurin, N, Bordon-Pallier, F, Cantalloube, C, Sans, S, Silve, S, Blanc, I, Fraisse, L, Rak, A, Jenner, L.B, Yusupova, G, Yusupov, M, Zhang, J, Kaneko, T, Yang, T.J, Fotouhi, N, Nuermberger, E, Tyagi, S, Betoudji, F, Upton, A, Sacchettini, J.C, Lagrange, S.Show

Cell ? ? ? (2023)

PMID: 36827973 DOI: 10.1016/j.cell.2023.01.043

Abstact

The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding in vitro and in vivo activity against Mycobacterium tuberculosis (Mtb). Sequanamycins are bacterial ribosome inhibitors that interact with the ribosome in a similar manner to classic macrolides like erythromycin and clarithromycin, but with binding characteristics that allow them to overcome the inherent macrolide resistance of Mtb. Structures of the ribosome with bound inhibitors were used to optimize sequanamycin to produce the advanced lead compound SEQ-9. SEQ-9 was efficacious in mouse models of acute and chronic TB as a single agent, and it demonstrated bactericidal activity in a murine TB infection model in combination with other TB drugs. These results support further investigation of this series as TB clinical candidates, with the potential for use in new regimens against drug-susceptible and drug-resistant TB.

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Primary Citation of related structures