8SYL

Cryo-EM structure of the Escherichia coli 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli, Escherichia phage T4
  • Mutation(s): Yes 

  • Deposited: 2023-05-25 Released: 2023-08-09 
  • Deposition Author(s): Seely, S.M., Gagnon, M.G.
  • Funding Organization(s): Other government, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.

Seely, S.M., Parajuli, N.P., De Tarafder, A., Ge, X., Sanyal, S., Gagnon, M.G.

(2023) Nat Commun 14: 4666-4666

  • DOI: https://doi.org/10.1038/s41467-023-40416-5
  • Primary Citation of Related Structures:  
    8EV6, 8EV7, 8SYL

  • PubMed Abstract: 

    Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N 1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3'-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.

    • Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]241Escherichia coliMutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3C [auth c]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]131Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]156Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]130Escherichia coliMutation(s): 0 
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Entity ID: 10
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30S ribosomal protein S10J [auth j]103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]129Escherichia coliMutation(s): 1 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14N [auth n]101Escherichia coliMutation(s): 0 
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Entity ID: 15
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30S ribosomal protein S15O [auth o]89Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]84Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]75Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]92Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]87Escherichia coliMutation(s): 0 
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Entity ID: 21
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30S ribosomal protein S21U [auth u]71Escherichia coliMutation(s): 0 
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50S ribosomal protein L2BA [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L4DA [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L5EA [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth G]177Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth L]142Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth M]123Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth N]144Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth O]136Escherichia coliMutation(s): 1 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth P]127Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18MA [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth R]115Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20OA [auth S]118Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21PA [auth T]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22QA [auth U]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23RA [auth V]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24SA [auth W]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25TA [auth X]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27UA [auth Y]85Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28VA [auth Z]78Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth 1]63Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth 2]59Escherichia coliMutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L31YA [auth 3]70Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32ZA [auth 4]57Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AB [auth 5]55Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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UniProt GroupP0A7N9
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth 6]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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UniProt GroupP0A7P5
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth 7]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DB [auth 8]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth a]1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
phenylalanine tRNAV [auth w],
X [auth y]		76Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
P-site initiator tRNAW [auth x]77Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
M-F-Stop mRNAY [auth v]24Escherichia phage T4
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S Ribosomal RNAZ [auth A]2,904Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S Ribosomal RNAAA [auth B]120Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKN
Query on AKN
Download Ideal Coordinates CCD File 
YE [auth a],
ZS [auth A]		(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
C22 H43 N5 O13
LKCWBDHBTVXHDL-RMDFUYIESA-N
PHE
Query on PHE
Download Ideal Coordinates CCD File 
ZE [auth w]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
MT [auth 3],
OT [auth 8]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth a]
AD [auth a]
AE [auth a]
AF [auth x]
AG [auth A]
AC [auth a],
AD [auth a],
AE [auth a],
AF [auth x],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth A],
AM [auth A],
AN [auth A],
AO [auth A],
AP [auth A],
AQ [auth A],
AR [auth A],
AS [auth A],
AT [auth B],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth x],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth A],
BM [auth A],
BN [auth A],
BO [auth A],
BP [auth A],
BQ [auth A],
BR [auth A],
BS [auth A],
BT [auth B],
CC [auth a],
CD [auth a],
CE [auth a],
CF [auth x],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth A],
CM [auth A],
CN [auth A],
CO [auth A],
CP [auth A],
CQ [auth A],
CR [auth A],
CS [auth A],
CT [auth B],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth v],
DG [auth A],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth A],
DM [auth A],
DN [auth A],
DO [auth A],
DP [auth A],
DQ [auth A],
DR [auth A],
DS [auth A],
DT [auth B],
EB [auth a],
EC [auth a],
ED [auth a],
EE [auth a],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth A],
EM [auth A],
EN [auth A],
EO [auth A],
EP [auth A],
EQ [auth A],
ER [auth A],
ES [auth A],
ET [auth B],
FB [auth a],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
FL [auth A],
FM [auth A],
FN [auth A],
FO [auth A],
FP [auth A],
FQ [auth A],
FR [auth A],
FS [auth A],
FT [auth B],
GB [auth a],
GC [auth a],
GD [auth a],
GE [auth a],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth A],
GM [auth A],
GN [auth A],
GO [auth A],
GP [auth A],
GQ [auth A],
GR [auth A],
GS [auth A],
GT [auth C],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HJ [auth A],
HK [auth A],
HL [auth A],
HM [auth A],
HN [auth A],
HO [auth A],
HP [auth A],
HQ [auth A],
HR [auth A],
HS [auth A],
HT [auth D],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth A],
IM [auth A],
IN [auth A],
IO [auth A],
IP [auth A],
IQ [auth A],
IR [auth A],
IS [auth A],
IT [auth P],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JJ [auth A],
JK [auth A],
JL [auth A],
JM [auth A],
JN [auth A],
JO [auth A],
JP [auth A],
JQ [auth A],
JR [auth A],
JS [auth A],
JT [auth S],
KB [auth a],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth A],
KM [auth A],
KN [auth A],
KO [auth A],
KP [auth A],
KQ [auth A],
KR [auth A],
KS [auth A],
KT [auth X],
LB [auth a],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
LL [auth A],
LM [auth A],
LN [auth A],
LO [auth A],
LP [auth A],
LQ [auth A],
LR [auth A],
LS [auth A],
LT [auth Y],
MB [auth a],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
ML [auth A],
MM [auth A],
MN [auth A],
MO [auth A],
MP [auth A],
MQ [auth A],
MR [auth A],
MS [auth A],
NB [auth a],
NC [auth a],
ND [auth a],
NE [auth a],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
NL [auth A],
NM [auth A],
NN [auth A],
NO [auth A],
NP [auth A],
NQ [auth A],
NR [auth A],
NS [auth A],
NT [auth 4],
OB [auth a],
OC [auth a],
OD [auth a],
OE [auth a],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth A],
OM [auth A],
ON [auth A],
OO [auth A],
OP [auth A],
OQ [auth A],
OR [auth A],
OS [auth A],
PB [auth a],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
PL [auth A],
PM [auth A],
PN [auth A],
PO [auth A],
PP [auth A],
PQ [auth A],
PR [auth A],
PS [auth A],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth A],
QN [auth A],
QO [auth A],
QP [auth A],
QQ [auth A],
QR [auth A],
QS [auth A],
RB [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth A],
RN [auth A],
RO [auth A],
RP [auth A],
RQ [auth A],
RR [auth A],
RS [auth A],
SB [auth a],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
SL [auth A],
SM [auth A],
SN [auth A],
SO [auth A],
SP [auth A],
SQ [auth A],
SR [auth A],
SS [auth A],
TB [auth a],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
TL [auth A],
TM [auth A],
TN [auth A],
TO [auth A],
TP [auth A],
TQ [auth A],
TR [auth A],
TS [auth A],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UL [auth A],
UM [auth A],
UN [auth A],
UO [auth A],
UP [auth A],
UQ [auth A],
UR [auth A],
US [auth A],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
VL [auth A],
VM [auth A],
VN [auth A],
VO [auth A],
VP [auth A],
VQ [auth A],
VR [auth A],
VS [auth A],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
WL [auth A],
WM [auth A],
WN [auth A],
WO [auth A],
WP [auth A],
WQ [auth A],
WR [auth A],
WS [auth A],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth A],
XL [auth A],
XM [auth A],
XN [auth A],
XO [auth A],
XP [auth A],
XQ [auth A],
XR [auth A],
XS [auth A],
YB [auth a],
YC [auth a],
YD [auth a],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth A],
YL [auth A],
YM [auth A],
YN [auth A],
YO [auth A],
YP [auth A],
YQ [auth A],
YR [auth A],
YS [auth A],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth A],
ZL [auth A],
ZM [auth A],
ZN [auth A],
ZO [auth A],
ZP [auth A],
ZQ [auth A],
ZR [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T		L [auth l]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		CA [auth D]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		KA [auth O]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2.4158
RECONSTRUCTIONcryoSPARC4.1.2

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentUniversity of Texas Medical Branch Startup Funds
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM136936
Welch FoundationUnited StatesH-2032-20200401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008280

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations, Refinement description