6XHX

Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with erythromycin and protein Y (YfiA) at 2.55A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Literature

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.

Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

(2021) Nat Chem Biol 17: 412-420

  • DOI: https://doi.org/10.1038/s41589-020-00715-0
  • Primary Citation of Related Structures:  
    6XHV, 6XHW, 6XHX, 6XHY

  • PubMed Abstract: 

    • Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases ...

    Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 Å resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally new explanation of how A2058 dimethylation confers resistance to macrolides. Moreover, high-resolution structures of two macrolide antibiotics bound to the unmodified ribosome reveal a previously unknown role of the desosamine moiety in drug binding, laying a foundation for the rational knowledge-based design of macrolides that can overcome Erm-mediated resistance.

    Organizational Affiliation: 

    Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA. yuryp@uic.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth 1D],
DB [auth 2D]		276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplB, TTHA1689
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth 1E],
EB [auth 2E]		206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplC, TTHA1692
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth 1F],
FB [auth 2F]		210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplD, TTHA1691
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth 1G],
GB [auth 2G]		182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplE, TTHA1680
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth 1H],
HB [auth 2H]		180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplF, TTHA1677
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth 1I],
IB [auth 2I]		148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplI, TTHA0242
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth 1N],
JB [auth 2N]		140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplM, TTHA1465
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth 1O],
KB [auth 2O]		122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplN, TTHA1682
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth 1P],
LB [auth 2P]		150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplO, TTHA1673
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth 1Q],
MB [auth 2Q]		141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplP, TTHA1685
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth 1R],
NB [auth 2R]		118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQ, rpl17, TTHA1663
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Entity ID: 14
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50S ribosomal protein L18N [auth 1S],
OB [auth 2S]		112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplR, TTHA1676
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth 1T],
PB [auth 2T]		146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplS, TTHA1031
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth 1U],
QB [auth 2U]		118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplT, TTHA0553
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth 1V],
RB [auth 2V]		101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplU, TTHA1783
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth 1W],
SB [auth 2W]		113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplV, TTHA1687
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth 1X],
TB [auth 2X]		96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplW, TTHA1690
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth 1Y],
UB [auth 2Y]		110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplX, TTHA1681
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth 1Z],
VB [auth 2Z]		206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplY, rpl25, rptL5, TTHA1589
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth 10],
WB [auth 20]		85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmA, TTHA1782
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth 11],
XB [auth 21]		98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmB, TTHA0042
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth 12],
YB [auth 22]		72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmC, TTHA1684
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth 13],
ZB [auth 23]		60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmD, TTHA1674
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Entity ID: 26
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50S ribosomal protein L31AC [auth 24],
Z [auth 14]		71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmE, TTHA1073
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MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 15],
BC [auth 25]		60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmF, rpl32, TTHA0418
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Entity ID: 28
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50S ribosomal protein L33BA [auth 16],
CC [auth 26]		54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmG, rpl33, TTHA0250
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 17],
DC [auth 27]		49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmH, rpl34, TTHA0446
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Entity ID: 30
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50S ribosomal protein L35DA [auth 18],
EC [auth 28]		65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmI, TTHA0552
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Entity ID: 31
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50S ribosomal protein L36EA [auth 19],
FC [auth 29]		37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJ, TTHA1668
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Entity ID: 33
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30S ribosomal protein S2GA [auth 1b],
HC [auth 2b]		256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsB, rps2, TTHA0861
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3HA [auth 1c],
IC [auth 2c]		239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsC, rps3, TTHA1686
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth 1d],
JC [auth 2d]		209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsD, rps4, TTHA1665
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30S ribosomal protein S5JA [auth 1e],
KC [auth 2e]		162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsE, TTHA1675
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth 1f],
LC [auth 2f]		101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsF, TTHA0245
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth 1g],
MC [auth 2g]		156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsG, rps7, TTHA1696
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8MA [auth 1h],
NC [auth 2h]		138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsH, TTHA1678
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth 1i],
OC [auth 2i]		128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsI, rps9, TTHA1464
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10OA [auth 1j],
PC [auth 2j]		105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJ, TTHA1693
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Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11PA [auth 1k],
QC [auth 2k]		129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsK, rps11, TTHA1666
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth 1l],
RC [auth 2l]		132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsL, TTHA1697
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Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth 1m],
SC [auth 2m]		126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsM, rps13, TTHA1667
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Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZSA [auth 1n],
TC [auth 2n]		61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZ, rpsN, TTHA1679
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Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth 1o],
UC [auth 2o]		89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsO, TTHA1138
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Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth 1p],
VC [auth 2p]		88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsP, TTHA1035
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth 1q],
WC [auth 2q]		105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQ, TTHA1683
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth 1r],
XC [auth 2r]		88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsR, TTHA0243
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Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth 1s],
YC [auth 2s]		93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsS, TTHA1688
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Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth 1t],
ZC [auth 2t]		106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsT, rps20, TTHA1397
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxAD [auth 2u],
ZA [auth 1u]		27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsU, TTHA1396
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Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-associated inhibitor AAB [auth 1y],
BD [auth 2y]		113Escherichia coli K-12Mutation(s): 0 
Gene Names: raiA, yfiA, b2597, JW2578
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Find proteins for P0AD49 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA [auth 1A],
BB [auth 2A]		2,915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAB [auth 1B],
CB [auth 2B]		121Thermus thermophilus HB8
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAFA [auth 1a],
GC [auth 2a]		1,521Thermus thermophilus HB8
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERY
Query on ERY
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IQA [auth 1A],
SKC [auth 2A]		ERYTHROMYCIN A
C37 H67 N O13
ULGZDMOVFRHVEP-RWJQBGPGSA-N		 Ligand Interaction
SF4
Query on SF4
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OHB [auth 1d],
VUC [auth 2d]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
ARG
Query on ARG
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JTA [auth 1F],
QRA [auth 1B]		ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O		 Ligand Interaction
MPD
Query on MPD
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HHB [auth 1a],
JQA [auth 1A],
NLC [auth 2B],
NUA [auth 1T],
QWA [auth 18],
HHB [auth 1a],
JQA [auth 1A],
NLC [auth 2B],
NUA [auth 1T],
QWA [auth 18],
TKC [auth 2A],
UKC [auth 2A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
ZN
Query on ZN
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AWA [auth 14],
CVC [auth 2n],
GIB [auth 1n],
GNC [auth 2Y],
HWA [auth 15],
AWA [auth 14],
CVC [auth 2n],
GIB [auth 1n],
GNC [auth 2Y],
HWA [auth 15],
IWA [auth 16],
JVA [auth 1Y],
LNC [auth 24],
ONC [auth 25],
PNC [auth 26],
SWA [auth 19],
TNC [auth 29]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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