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 report that the aromatic polyketide antibiotic tetracenomycin (TcmX) is a potent inhibitor of protein synthesis, and does not induce DNA damage as previously thought ...

    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 L8D [auth LA]248Homo sapiensMutation(s): 0 
Gene Names: RPL8
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GTEx:  ENSG00000161016 
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Entity ID: 5
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60S ribosomal protein L3E [auth LB]397Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
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GTEx:  ENSG00000100316 
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Entity ID: 6
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60S ribosomal protein L4F [auth LC]368Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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GTEx:  ENSG00000174444 
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Entity ID: 7
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60S ribosomal protein L5G [auth LD]293Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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Entity ID: 8
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60S ribosomal protein L6H [auth LE]247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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60S ribosomal protein L7I [auth LF]225Homo sapiensMutation(s): 0 
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Entity ID: 10
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60S ribosomal protein L7aJ [auth LG]241Homo sapiensMutation(s): 0 
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60S ribosomal protein L9K [auth LH]190Homo sapiensMutation(s): 0 
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60S ribosomal protein L10-likeL [auth LI]213Homo sapiensMutation(s): 0 
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60S ribosomal protein L11M [auth LJ]176Homo sapiensMutation(s): 0 
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60S ribosomal protein L13N [auth LL]210Homo sapiensMutation(s): 0 
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60S ribosomal protein L14O [auth LM]139Homo sapiensMutation(s): 0 
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60S ribosomal protein L15P [auth LN]203Homo sapiensMutation(s): 0 
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60S ribosomal protein L13aQ [auth LO]201Homo sapiensMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L17R [auth LP]153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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Entity ID: 19
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60S ribosomal protein L18S [auth LQ]187Homo sapiensMutation(s): 0 
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60S ribosomal protein L19T [auth LR]187Homo sapiensMutation(s): 0 
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60S ribosomal protein L18aU [auth LS]175Homo sapiensMutation(s): 0 
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60S ribosomal protein L21V [auth LT]159Homo sapiensMutation(s): 0 
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60S ribosomal protein L22W [auth LU]99Homo sapiensMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L23X [auth LV]131Homo sapiensMutation(s): 0 
Gene Names: RPL23
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60S ribosomal protein L24Y [auth LW]124Homo sapiensMutation(s): 0 
Gene Names: RPL24
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Entity ID: 26
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60S ribosomal protein L23aZ [auth LX]120Homo sapiensMutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L26AA [auth LY]134Homo sapiensMutation(s): 0 
Gene Names: RPL26
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60S ribosomal protein L27BA [auth LZ]135Homo sapiensMutation(s): 0 
Gene Names: RPL27
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60S ribosomal protein L27aCA [auth La]147Homo sapiensMutation(s): 0 
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60S ribosomal protein L29DA [auth Lb]121Homo sapiensMutation(s): 0 
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60S ribosomal protein L30EA [auth Lc]98Homo sapiensMutation(s): 0 
Gene Names: RPL30
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60S ribosomal protein L31FA [auth Ld]107Homo sapiensMutation(s): 0 
Gene Names: RPL31
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60S ribosomal protein L32GA [auth Le]128Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
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GTEx:  ENSG00000144713 
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60S ribosomal protein L35aHA [auth Lf]109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
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GTEx:  ENSG00000182899 
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60S ribosomal protein L34IA [auth Lg]114Homo sapiensMutation(s): 0 
Gene Names: RPL34
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Entity ID: 36
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60S ribosomal protein L35JA [auth Lh]122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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Entity ID: 37
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60S ribosomal protein L36KA [auth Li]102Homo sapiensMutation(s): 0 
Gene Names: RPL36
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60S ribosomal protein L37LA [auth Lj]86Homo sapiensMutation(s): 0 
Gene Names: RPL37
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Entity ID: 39
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60S ribosomal protein L38MA [auth Lk]69Homo sapiensMutation(s): 0 
Gene Names: RPL38
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GTEx:  ENSG00000172809 
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Entity ID: 40
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60S ribosomal protein L39NA [auth Ll]50Homo sapiensMutation(s): 0 
Gene Names: RPL39
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GTEx:  ENSG00000198918 
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Entity ID: 41
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Ubiquitin-60S ribosomal protein L40OA [auth Lm]52Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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Find proteins for P62987 (Homo sapiens)
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PHAROS:  P62987
GTEx:  ENSG00000221983 
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UniProt GroupP62987
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41PA [auth Ln]24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Find proteins for P62945 (Homo sapiens)
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PHAROS:  P62945
GTEx:  ENSG00000229117 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36aQA [auth Lo]105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
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Find proteins for P83881 (Homo sapiens)
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PHAROS:  P83881
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37aRA [auth Lp]91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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Find proteins for P61513 (Homo sapiens)
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PHAROS:  P61513
GTEx:  ENSG00000197756 
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UniProt GroupP61513
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28SA [auth Lr]125Homo sapiensMutation(s): 0 
Gene Names: RPL28
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Find proteins for P46779 (Homo sapiens)
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PHAROS:  P46779
GTEx:  ENSG00000108107 
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UniProt GroupP46779
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10aTA [auth Lz]217Homo sapiensMutation(s): 0 
Gene Names: RPL10ANEDD6
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Find proteins for P62906 (Homo sapiens)
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PHAROS:  P62906
GTEx:  ENSG00000198755 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA [auth L5]3773Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth L7]120Homo sapiens
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAC [auth L8]156Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCW (Subject of Investigation/LOI)
Query on OCW

Download Ideal Coordinates CCD File 
AJ [auth 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

Download Ideal Coordinates CCD File 
PJ [auth Lg],
RJ [auth Lj],
SJ [auth Lm],
TJ [auth Lo],
UJ [auth Lp]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth L5],
AC [auth L5],
AD [auth L5],
AE [auth L5],
AF [auth L5],
AB [auth L5],
AC [auth L5],
AD [auth L5],
AE [auth L5],
AF [auth L5],
AG [auth L5],
AH [auth L5],
AI [auth L5],
BB [auth L5],
BC [auth L5],
BD [auth L5],
BE [auth L5],
BF [auth L5],
BG [auth L5],
BH [auth L5],
BI [auth L5],
BJ [auth L7],
CB [auth L5],
CC [auth L5],
CD [auth L5],
CE [auth L5],
CF [auth L5],
CG [auth L5],
CH [auth L5],
CI [auth L5],
CJ [auth L7],
DB [auth L5],
DC [auth L5],
DD [auth L5],
DE [auth L5],
DF [auth L5],
DG [auth L5],
DH [auth L5],
DI [auth L5],
DJ [auth L7],
EB [auth L5],
EC [auth L5],
ED [auth L5],
EE [auth L5],
EF [auth L5],
EG [auth L5],
EH [auth L5],
EI [auth L5],
EJ [auth L8],
FB [auth L5],
FC [auth L5],
FD [auth L5],
FE [auth L5],
FF [auth L5],
FG [auth L5],
FH [auth L5],
FI [auth L5],
FJ [auth L8],
GB [auth L5],
GC [auth L5],
GD [auth L5],
GE [auth L5],
GF [auth L5],
GG [auth L5],
GH [auth L5],
GI [auth L5],
GJ [auth L8],
HB [auth L5],
HC [auth L5],
HD [auth L5],
HE [auth L5],
HF [auth L5],
HG [auth L5],
HH [auth L5],
HI [auth L5],
HJ [auth L8],
IB [auth L5],
IC [auth L5],
ID [auth L5],
IE [auth L5],
IF [auth L5],
IG [auth L5],
IH [auth L5],
II [auth L5],
IJ [auth LA],
JB [auth L5],
JC [auth L5],
JD [auth L5],
JE [auth L5],
JF [auth L5],
JG [auth L5],
JH [auth L5],
JI [auth L5],
JJ [auth LI],
KB [auth L5],
KC [auth L5],
KD [auth L5],
KE [auth L5],
KF [auth L5],
KG [auth L5],
KH [auth L5],
KI [auth L5],
KJ [auth LP],
LB [auth L5],
LC [auth L5],
LD [auth L5],
LE [auth L5],
LF [auth L5],
LG [auth L5],
LH [auth L5],
LI [auth L5],
LJ [auth LT],
MB [auth L5],
MC [auth L5],
MD [auth L5],
ME [auth L5],
MF [auth L5],
MG [auth L5],
MH [auth L5],
MI [auth L5],
MJ [auth LV],
NB [auth L5],
NC [auth L5],
ND [auth L5],
NE [auth L5],
NF [auth L5],
NG [auth L5],
NH [auth L5],
NI [auth L5],
NJ [auth Le],
OB [auth L5],
OC [auth L5],
OD [auth L5],
OE [auth L5],
OF [auth L5],
OG [auth L5],
OH [auth L5],
OI [auth L5],
OJ [auth Lg],
PB [auth L5],
PC [auth L5],
PD [auth L5],
PE [auth L5],
PF [auth L5],
PG [auth L5],
PH [auth L5],
PI [auth L5],
QB [auth L5],
QC [auth L5],
QD [auth L5],
QE [auth L5],
QF [auth L5],
QG [auth L5],
QH [auth L5],
QI [auth L5],
QJ [auth Lj],
RB [auth L5],
RC [auth L5],
RD [auth L5],
RE [auth L5],
RF [auth L5],
RG [auth L5],
RH [auth L5],
RI [auth L5],
SB [auth L5],
SC [auth L5],
SD [auth L5],
SE [auth L5],
SF [auth L5],
SG [auth L5],
SH [auth L5],
SI [auth L5],
TB [auth L5],
TC [auth L5],
TD [auth L5],
TE [auth L5],
TF [auth L5],
TG [auth L5],
TH [auth L5],
TI [auth L5],
UA [auth L5],
UB [auth L5],
UC [auth L5],
UD [auth L5],
UE [auth L5],
UF [auth L5],
UG [auth L5],
UH [auth L5],
UI [auth L5],
VA [auth L5],
VB [auth L5],
VC [auth L5],
VD [auth L5],
VE [auth L5],
VF [auth L5],
VG [auth L5],
VH [auth L5],
VI [auth L5],
WA [auth L5],
WB [auth L5],
WC [auth L5],
WD [auth L5],
WE [auth L5],
WF [auth L5],
WG [auth L5],
WH [auth L5],
WI [auth L5],
XA [auth L5],
XB [auth L5],
XC [auth L5],
XD [auth L5],
XE [auth L5],
XF [auth L5],
XG [auth L5],
XH [auth L5],
XI [auth L5],
YA [auth L5],
YB [auth L5],
YC [auth L5],
YD [auth L5],
YE [auth L5],
YF [auth L5],
YG [auth L5],
YH [auth L5],
YI [auth L5],
ZA [auth L5],
ZB [auth L5],
ZC [auth L5],
ZD [auth L5],
ZE [auth L5],
ZF [auth L5],
ZG [auth L5],
ZH [auth L5],
ZI [auth L5]
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

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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