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



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 

  • DOI: 10.1038/s41589-020-0578-x
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
60S ribosomal protein L8LA248Homo sapiensMutation(s): 0 
Gene Names: RPL8
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PHAROS  P62917
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3LB397Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
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PHAROS  P39023
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4LC368Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6LE247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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PHAROS  Q02878
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11LJ176Homo sapiensMutation(s): 0 
Gene Names: RPL11
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13LL210Homo sapiensMutation(s): 0 
Gene Names: RPL13BBC1OK/SW-cl.46
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14LM139Homo sapiensMutation(s): 0 
Gene Names: RPL14
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15LN203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13aLO201Homo sapiensMutation(s): 0 
Gene Names: RPL13A
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18LQ187Homo sapiensMutation(s): 0 
Gene Names: RPL18
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21LT159Homo sapiensMutation(s): 0 
Gene Names: RPL21
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22LU99Homo sapiensMutation(s): 0 
Gene Names: RPL22
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23aLX120Homo sapiensMutation(s): 0 
Gene Names: RPL23A
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27aLa147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30Lc98Homo sapiensMutation(s): 0 
Gene Names: RPL30
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31Ld107Homo sapiensMutation(s): 0 
Gene Names: RPL31
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32Le128Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36Li102Homo sapiensMutation(s): 0 
Gene Names: RPL36
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38Lk69Homo sapiensMutation(s): 0 
Gene Names: RPL38
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39Ll50Homo sapiensMutation(s): 0 
Gene Names: RPL39
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37aLp91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28Lr125Homo sapiensMutation(s): 0 
Gene Names: RPL28
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10aLz217Homo sapiensMutation(s): 0 
Gene Names: RPL10ANEDD6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7aLG241Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9LH190Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10-likeLI213Homo sapiensMutation(s): 0 
Gene Names: RPL10L
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17LP153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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PHAROS  P18621
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19LR187Homo sapiensMutation(s): 0 
Gene Names: RPL19
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PHAROS  P84098
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18aLS175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23LV131Homo sapiensMutation(s): 0 
Gene Names: RPL23
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24LW124Homo sapiensMutation(s): 0 
Gene Names: RPL24
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26LY134Homo sapiensMutation(s): 0 
Gene Names: RPL26
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27LZ135Homo sapiensMutation(s): 0 
Gene Names: RPL27
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29Lb121Homo sapiensMutation(s): 0 
Gene Names: RPL29
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35aLf109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34Lg114Homo sapiensMutation(s): 0 
Gene Names: RPL34
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35Lh122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37Lj86Homo sapiensMutation(s): 0 
Gene Names: RPL37
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40Lm52Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41Ln24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36aLo105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5LD293Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7LF225Homo sapiensMutation(s): 0 
Gene Names: RPL7
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Entity ID: 1
MoleculeChainsLengthOrganism
28S ribosomal RNAL53773Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAL7120Homo sapiens

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Entity ID: 3
MoleculeChainsLengthOrganism
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