6Y6X image
Entry Detail
PDB ID:
6Y6X
EMDB ID:
Keywords:
Title:
Tetracenomycin X bound to the human ribosome
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-02-27
Release Date:
2020-07-08
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:28S ribosomal RNA
Chain IDs:A (auth: L5)
Chain Length:5069
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:B (auth: L7)
Chain Length:120
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:C (auth: L8)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:D (auth: LA)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:E (auth: LB)
Chain Length:397
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:F (auth: LC)
Chain Length:368
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:G (auth: LD)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:H (auth: LE)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7
Chain IDs:I (auth: LF)
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:J (auth: LG)
Chain Length:241
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:K (auth: LH)
Chain Length:122
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10-like
Chain IDs:L (auth: LI)
Chain Length:213
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:M (auth: LJ)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:N (auth: LL)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:O (auth: LM)
Chain Length:52
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15
Chain IDs:P (auth: LN)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13a
Chain IDs:Q (auth: LO)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:R (auth: LP)
Chain Length:91
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18
Chain IDs:S (auth: LQ)
Chain Length:187
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:T (auth: LR)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:U (auth: LS)
Chain Length:175
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:V (auth: LT)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22
Chain IDs:W (auth: LU)
Chain Length:99
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:X (auth: LV)
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24
Chain IDs:Y (auth: LW)
Chain Length:124
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23a
Chain IDs:Z (auth: LX)
Chain Length:120
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:AA (auth: LY)
Chain Length:134
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:BA (auth: LZ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:CA (auth: La)
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:DA (auth: Lb)
Chain Length:397
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:EA (auth: Lc)
Chain Length:368
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:FA (auth: Ld)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:GA (auth: Le)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:HA (auth: Lf)
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:IA (auth: Lg)
Chain Length:241
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:JA (auth: Lh)
Chain Length:122
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:KA (auth: Li)
Chain Length:213
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:LA (auth: Lj)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:MA (auth: Lk)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:NA (auth: Ll)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:OA (auth: Lm)
Chain Length:52
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:PA (auth: Ln)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36a
Chain IDs:QA (auth: Lo)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37a
Chain IDs:RA (auth: Lp)
Chain Length:91
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:SA (auth: Lr)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10a
Chain IDs:TA (auth: Lz)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation

Abstact

The increase in multi-drug resistant pathogenic bacteria is making our current arsenal of clinically used antibiotics obsolete, highlighting the urgent need for new lead compounds with distinct target binding sites to avoid cross-resistance. Here we report that the aromatic polyketide antibiotic tetracenomycin (TcmX) is a potent inhibitor of protein synthesis, and does not induce DNA damage as previously thought. Despite the structural similarity to the well-known translation inhibitor tetracycline, we show that TcmX does not interact with the small ribosomal subunit, but rather binds to the large subunit, within the polypeptide exit tunnel. This previously unappreciated binding site is located adjacent to the macrolide-binding site, where TcmX stacks on the noncanonical basepair formed by U1782 and U2586 of the 23S ribosomal RNA. Although the binding site is distinct from the macrolide antibiotics, our results indicate that like macrolides, TcmX allows translation of short oligopeptides before further translation is blocked.

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Disease

Primary Citation of related structures