6XHV

Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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: 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],
GB [auth 2D]
276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth 1E],
HB [auth 2E]
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth 1F],
IB [auth 2F]
210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth 1G],
JB [auth 2G]
182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth 1H],
KB [auth 2H]
180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth 1I],
LB [auth 2I]
148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth 1N],
MB [auth 2N]
140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth 1O],
NB [auth 2O]
122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth 1P],
OB [auth 2P]
150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth 1Q],
PB [auth 2Q]
141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth 1R],
QB [auth 2R]
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth 1S],
RB [auth 2S]
112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth 1T],
SB [auth 2T]
146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth 1U],
TB [auth 2U]
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth 1V],
UB [auth 2V]
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth 1W],
VB [auth 2W]
113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth 1X],
WB [auth 2X]
96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth 1Y],
XB [auth 2Y]
110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth 1Z],
YB [auth 2Z]
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth 10],
ZB [auth 20]
85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth 11],
AC [auth 21]
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth 12],
BC [auth 22]
72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth 13],
CC [auth 23]
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31Z [auth 14],
DC [auth 24]
71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 15],
EC [auth 25]
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 28
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50S ribosomal protein L33BA [auth 16],
FC [auth 26]
54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 17],
GC [auth 27]
49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 18],
HC [auth 28]
65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
UniProt
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Entity ID: 31
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50S ribosomal protein L36EA [auth 19],
IC [auth 29]
37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 33
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30S ribosomal protein S2GA [auth 1b],
KC [auth 2b]
256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 34
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30S ribosomal protein S3HA [auth 1c],
LC [auth 2c]
239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 35
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30S ribosomal protein S4IA [auth 1d],
MC [auth 2d]
209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5JA [auth 1e],
NC [auth 2e]
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth 1f],
OC [auth 2f]
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth 1g],
PC [auth 2g]
156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 39
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30S ribosomal protein S8MA [auth 1h],
QC [auth 2h]
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth 1i],
RC [auth 2i]
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
UniProt
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Entity ID: 41
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30S ribosomal protein S10OA [auth 1j],
SC [auth 2j]
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
UniProt
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],
TC [auth 2k]
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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],
UC [auth 2l]
132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
UniProt
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],
VC [auth 2m]
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
UniProt
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZSA [auth 1n],
WC [auth 2n]
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
UniProt
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],
XC [auth 2o]
89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
UniProt
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],
YC [auth 2p]
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth 1q],
ZC [auth 2q]
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
UniProt
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth 1r],
AD [auth 2r]
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
UniProt
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],
BD [auth 2s]
93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
UniProt
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],
CD [auth 2t]
106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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 ThxZA [auth 1u],
DD [auth 2u]
27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA [auth 1A],
EB [auth 2A]
2915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAB [auth 1B],
FB [auth 2B]
121Thermus thermophilus HB8
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAFA [auth 1a],
JC [auth 2a]
1521Thermus thermophilus HB8
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Entity ID: 53
MoleculeChainsLengthOrganismImage
mRNAAB [auth 1v],
ED [auth 2v]
24Escherichia virus T4
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Entity ID: 54
MoleculeChainsLengthOrganismImage
A-site tRNABB [auth 1w],
FD [auth 2w]
76Escherichia coli
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Entity ID: 55
MoleculeChainsLengthOrganismImage
P-site tRNACB [auth 1x],
GD [auth 2x]
77Escherichia coli
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Entity ID: 56
MoleculeChainsLengthOrganismImage
E-site tRNADB [auth 1y],
HD [auth 2y]
76Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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JKB [auth 1d],
SGD [auth 2d]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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CHD [auth 2n],
EXC [auth 25],
FBB [auth 15],
GXC [auth 26],
HBB [auth 16],
CHD [auth 2n],
EXC [auth 25],
FBB [auth 15],
GXC [auth 26],
HBB [auth 16],
LXC [auth 29],
QWC [auth 2Y],
TKB [auth 1n],
UBB [auth 19],
XAB [auth 14],
XZA [auth 1Y],
YWC [auth 24]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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AZ [auth 1A],
IEC [auth 2A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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