6Y6X

Tetracenomycin X bound to the human ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel.

Osterman, I.A., Wieland, M., Maviza, T.P., Lashkevich, K.A., Lukianov, D.A., Komarova, E.S., Zakalyukina, Y.V., Buschauer, R., Shiriaev, D.I., Leyn, S.A., Zlamal, J.E., Biryukov, M.V., Skvortsov, D.A., Tashlitsky, V.N., Polshakov, V.I., Cheng, J., Polikanov, Y.S., Bogdanov, A.A., Osterman, A.L., Dmitriev, S.E., Beckmann, R., Dontsova, O.A., Wilson, D.N., Sergiev, P.V.

(2020) Nat Chem Biol 16: 1071-1077

  • DOI: 10.1038/s41589-020-0578-x
  • Primary Citation of Related Structures:  
    6Y69, 6Y6X

  • PubMed Abstract: 

    • 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 repo ...

    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.

    Organizational Affiliation: 

    Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia. petya@genebee.msu.su.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8 LA248Homo sapiensMutation(s): 0 
Gene Names: RPL8
Find proteins for P62917 (Homo sapiens)
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GTEx:  ENSG00000161016
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3 LB397Homo sapiensMutation(s): 0 
Gene Names: RPL3, OK/SW-cl.32
Find proteins for P39023 (Homo sapiens)
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PHAROS:  P39023
GTEx:  ENSG00000100316
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4 LC368Homo sapiensMutation(s): 0 
Gene Names: RPL4, RPL1
Find proteins for P36578 (Homo sapiens)
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GTEx:  ENSG00000174444
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5 LD293Homo sapiensMutation(s): 0 
Gene Names: RPL5, MSTP030
Find proteins for P46777 (Homo sapiens)
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GTEx:  ENSG00000122406
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6 LE247Homo sapiensMutation(s): 0 
Gene Names: RPL6, TXREB1
Find proteins for Q02878 (Homo sapiens)
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GTEx:  ENSG00000089009
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Entity ID: 9
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60S ribosomal protein L7 LF225Homo sapiensMutation(s): 0 
Gene Names: RPL7
Find proteins for P18124 (Homo sapiens)
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GTEx:  ENSG00000147604
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7a LG241Homo sapiensMutation(s): 0 
Gene Names: RPL7A, SURF-3, SURF3
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GTEx:  ENSG00000148303
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Entity ID: 11
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60S ribosomal protein L9 LH190Homo sapiensMutation(s): 0 
Gene Names: RPL9, OK/SW-cl.103, RPL9P7, RPL9P8, RPL9P9
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GTEx:  ENSG00000163682
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10-like LI213Homo sapiensMutation(s): 0 
Gene Names: RPL10L
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GTEx:  ENSG00000165496
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Entity ID: 13
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60S ribosomal protein L11 LJ176Homo sapiensMutation(s): 0 
Gene Names: RPL11
Find proteins for P62913 (Homo sapiens)
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GTEx:  ENSG00000142676
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Entity ID: 14
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60S ribosomal protein L13 LL210Homo sapiensMutation(s): 0 
Gene Names: RPL13, BBC1, OK/SW-cl.46
Find proteins for P26373 (Homo sapiens)
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GTEx:  ENSG00000167526
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Entity ID: 15
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60S ribosomal protein L14 LM139Homo sapiensMutation(s): 0 
Gene Names: RPL14
Find proteins for P50914 (Homo sapiens)
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GTEx:  ENSG00000188846
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Entity ID: 16
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60S ribosomal protein L15 LN203Homo sapiensMutation(s): 0 
Gene Names: RPL15, EC45, TCBAP0781
Find proteins for P61313 (Homo sapiens)
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GTEx:  ENSG00000174748
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Entity ID: 17
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60S ribosomal protein L13a LO201Homo sapiensMutation(s): 0 
Gene Names: RPL13A
Find proteins for P40429 (Homo sapiens)
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GTEx:  ENSG00000142541
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Entity ID: 18
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60S ribosomal protein L17 LP153Homo sapiensMutation(s): 0 
Gene Names: RPL17
Find proteins for P18621 (Homo sapiens)
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GTEx:  ENSG00000265681
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18 LQ187Homo sapiensMutation(s): 0 
Gene Names: RPL18
Find proteins for Q07020 (Homo sapiens)
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GTEx:  ENSG00000063177
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Entity ID: 20
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60S ribosomal protein L19 LR187Homo sapiensMutation(s): 0 
Gene Names: RPL19
Find proteins for P84098 (Homo sapiens)
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GTEx:  ENSG00000108298
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Entity ID: 21
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60S ribosomal protein L18a LS175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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GTEx:  ENSG00000105640
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Entity ID: 22
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60S ribosomal protein L21 LT159Homo sapiensMutation(s): 0 
Gene Names: RPL21
Find proteins for P46778 (Homo sapiens)
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GTEx:  ENSG00000122026
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Entity ID: 23
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60S ribosomal protein L22 LU99Homo sapiensMutation(s): 0 
Gene Names: RPL22
Find proteins for P35268 (Homo sapiens)
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GTEx:  ENSG00000116251
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Entity ID: 24
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60S ribosomal protein L23 LV131Homo sapiensMutation(s): 0 
Gene Names: RPL23
Find proteins for P62829 (Homo sapiens)
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GTEx:  ENSG00000125691
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Entity ID: 25
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60S ribosomal protein L24 LW124Homo sapiensMutation(s): 0 
Gene Names: RPL24
Find proteins for P83731 (Homo sapiens)
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GTEx:  ENSG00000114391
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Entity ID: 26
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60S ribosomal protein L23a LX120Homo sapiensMutation(s): 0 
Gene Names: RPL23A
Find proteins for P62750 (Homo sapiens)
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GTEx:  ENSG00000198242
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26 LY134Homo sapiensMutation(s): 0 
Gene Names: RPL26
Find proteins for P61254 (Homo sapiens)
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GTEx:  ENSG00000161970
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Entity ID: 28
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60S ribosomal protein L27 LZ135Homo sapiensMutation(s): 0 
Gene Names: RPL27
Find proteins for P61353 (Homo sapiens)
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GTEx:  ENSG00000131469
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Entity ID: 29
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60S ribosomal protein L27a La147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
Find proteins for P46776 (Homo sapiens)
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GTEx:  ENSG00000166441
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29 Lb121Homo sapiensMutation(s): 0 
Gene Names: RPL29
Find proteins for P47914 (Homo sapiens)
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GTEx:  ENSG00000162244
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30 Lc98Homo sapiensMutation(s): 0 
Gene Names: RPL30
Find proteins for P62888 (Homo sapiens)
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GTEx:  ENSG00000156482
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31 Ld107Homo sapiensMutation(s): 0 
Gene Names: RPL31
Find proteins for P62899 (Homo sapiens)
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GTEx:  ENSG00000071082
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32 Le128Homo sapiensMutation(s): 0 
Gene Names: RPL32, PP9932
Find proteins for P62910 (Homo sapiens)
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GTEx:  ENSG00000144713
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35a Lf109Homo sapiensMutation(s): 0 
Gene Names: RPL35A, GIG33
Find proteins for P18077 (Homo sapiens)
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GTEx:  ENSG00000182899
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34 Lg114Homo sapiensMutation(s): 0 
Gene Names: RPL34
Find proteins for P49207 (Homo sapiens)
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GTEx:  ENSG00000109475
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35 Lh122Homo sapiensMutation(s): 0 
Gene Names: RPL35
Find proteins for P42766 (Homo sapiens)
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GTEx:  ENSG00000136942
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36 Li102Homo sapiensMutation(s): 0 
Gene Names: RPL36
Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS:  Q9Y3U8
GTEx:  ENSG00000130255
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37 Lj86Homo sapiensMutation(s): 0 
Gene Names: RPL37
Find proteins for P61927 (Homo sapiens)
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GTEx:  ENSG00000145592
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38 Lk69Homo sapiensMutation(s): 0 
Gene Names: RPL38
Find proteins for P63173 (Homo sapiens)
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GTEx:  ENSG00000172809
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39 Ll50Homo sapiensMutation(s): 0 
Gene Names: RPL39
Find proteins for P62891 (Homo sapiens)
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GTEx:  ENSG00000198918
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Entity ID: 41
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Ubiquitin-60S ribosomal protein L40 Lm52Homo sapiensMutation(s): 0 
Gene Names: UBA52, UBCEP2
Find proteins for P62987 (Homo sapiens)
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PHAROS:  P62987
GTEx:  ENSG00000221983
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41 Ln24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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GTEx:  ENSG00000229117
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36a Lo105Homo sapiensMutation(s): 0 
Gene Names: RPL36A, RPL44, GIG15, MIG6
Find proteins for P83881 (Homo sapiens)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37a Lp91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
Find proteins for P61513 (Homo sapiens)
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GTEx:  ENSG00000197756
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28 Lr125Homo sapiensMutation(s): 0 
Gene Names: RPL28
Find proteins for P46779 (Homo sapiens)
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GTEx:  ENSG00000108107
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Entity ID: 46
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60S ribosomal protein L10a Lz217Homo sapiensMutation(s): 0 
Gene Names: RPL10A, NEDD6
Find proteins for P62906 (Homo sapiens)
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GTEx:  ENSG00000198755
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S ribosomal RNAL53773Homo sapiens
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Entity ID: 2
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5S ribosomal RNAL7120Homo sapiens
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAL8156Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCW
Query on OCW
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L5
methyl (6~{a}~{R},7~{S},10~{a}~{R})-3,8,10~{a}-trimethoxy-1-methyl-6~{a},7,12-tris(oxidanyl)-6,10,11-tris(oxidanylidene)-7~{H}-tetracene-2-carboxylate
C24 H22 O11
QSPIPUXWSNFXCK-AGILITTLSA-N		 Ligand Interaction
ZN
Query on ZN
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Lg, Lj, Lm, Lo, Lp
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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L5, L7, L8, LA, LI, LP, LT, LV, Le, Lg, Lj
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references