7S1G

wild-type Escherichia coli stalled ribosome with antibiotic linezolid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.

Tsai, K.Stojkovic, V.Lee, D.J.Young, I.D.Szal, T.Klepacki, D.Vazquez-Laslop, N.Mankin, A.S.Fraser, J.S.Fujimori, D.G.

(2022) Nat Struct Mol Biol 29: 162-171

  • DOI: https://doi.org/10.1038/s41594-022-00723-9
  • Primary Citation of Related Structures:  
    7S1G, 7S1H, 7S1I, 7S1J, 7S1K

  • PubMed Abstract: 

    The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. However, the molecular basis for context-specificity has not been elucidated. Here we show that the second-generation oxazolidinone radezolid also induces stalling with a penultimate alanine, and we determine high-resolution cryo-EM structures of linezolid- and radezolid-stalled ribosome complexes to explain their mechanism of action. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling due to repositioning of the modified nucleotide. Together, our findings provide molecular understanding for the context-specificity of oxazolidinones.


  • Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19A [auth 1]92Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20B [auth 2]87Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21C [auth 3]71Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth D]240Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3H [auth E]233Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4I [auth F]206Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5J [auth G]167Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6K [auth H]135Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L2N [auth K]273Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L3O [auth L]209Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L4P [auth M]201Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5Q [auth N]179Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L6R [auth O]177Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L9S [auth P]149Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31T [auth Q]70Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13U [auth R]142Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14V [auth S]123Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15W [auth T]144Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16X [auth U]136Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L17Y [auth V]127Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Z [auth W]117Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19AA [auth X]115Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20BA [auth Y]118Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21CA [auth Z]103Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22DA [auth a]110Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23EA [auth b]100Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24FA [auth c]104Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25GA [auth d]94Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27HA [auth e]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28IA [auth f]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29JA [auth g]63Escherichia coliMutation(s): 0 
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Entity ID: 37
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50S ribosomal protein L30KA [auth h]59Escherichia coliMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L32LA [auth i]57Escherichia coliMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L33MA [auth j]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34NA [auth k]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35OA [auth l]65Escherichia coliMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L36PA [auth m]38Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7QA [auth n]179Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8RA [auth o]130Escherichia coliMutation(s): 0 
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Entity ID: 45
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30S ribosomal protein S9SA [auth p]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10TA [auth q]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11UA [auth r]129Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
nascent peptide chainVA [auth s]5Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12WA [auth t]124Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13XA [auth u]118Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14YA [auth v]101Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15ZA [auth w]89Escherichia coliMutation(s): 0 
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Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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UniProt GroupP0ADZ4
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16AB [auth x]82Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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UniProt GroupP0A7T3
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17BB [auth y]84Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18CB [auth z]75Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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UniProt GroupP0A7T7
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Entity ID: 4
MoleculeChains LengthOrganismImage
mRNAD [auth 4]15Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
tRNA(PHE)E [auth A]76Escherichia coli
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S rRNAF [auth C]1,540Escherichia coli
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Entity ID: 12
MoleculeChains LengthOrganismImage
23S rRNAL [auth I]2,904Escherichia coli
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Entity ID: 13
MoleculeChains LengthOrganismImage
5S rRNAM [auth J]120Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZLD (Subject of Investigation/LOI)
Query on ZLD

Download Ideal Coordinates CCD File 
OI [auth I]N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide
C16 H20 F N3 O4
TYZROVQLWOKYKF-ZDUSSCGKSA-N
ZN
Query on ZN

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RI [auth Q],
TI [auth m]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth C]
AD [auth C]
AE [auth C]
AF [auth I]
AG [auth I]
AC [auth C],
AD [auth C],
AE [auth C],
AF [auth I],
AG [auth I],
AH [auth I],
AI [auth I],
BC [auth C],
BD [auth C],
BE [auth C],
BF [auth I],
BG [auth I],
BH [auth I],
BI [auth I],
CC [auth C],
CD [auth C],
CE [auth C],
CF [auth I],
CG [auth I],
CH [auth I],
CI [auth I],
DB [auth C],
DC [auth C],
DD [auth C],
DE [auth C],
DF [auth I],
DG [auth I],
DH [auth I],
DI [auth I],
EB [auth C],
EC [auth C],
ED [auth C],
EE [auth C],
EF [auth I],
EG [auth I],
EH [auth I],
EI [auth I],
FB [auth C],
FC [auth C],
FD [auth C],
FE [auth C],
FF [auth I],
FG [auth I],
FH [auth I],
FI [auth I],
GB [auth C],
GC [auth C],
GD [auth C],
GE [auth C],
GF [auth I],
GG [auth I],
GH [auth I],
GI [auth I],
HB [auth C],
HC [auth C],
HD [auth C],
HE [auth C],
HF [auth I],
HG [auth I],
HH [auth I],
HI [auth I],
IB [auth C],
IC [auth C],
ID [auth C],
IE [auth I],
IF [auth I],
IG [auth I],
IH [auth I],
II [auth I],
JB [auth C],
JC [auth C],
JD [auth C],
JE [auth I],
JF [auth I],
JG [auth I],
JH [auth I],
JI [auth I],
KB [auth C],
KC [auth C],
KD [auth C],
KE [auth I],
KF [auth I],
KG [auth I],
KH [auth I],
KI [auth I],
LB [auth C],
LC [auth C],
LD [auth C],
LE [auth I],
LF [auth I],
LG [auth I],
LH [auth I],
LI [auth I],
MB [auth C],
MC [auth C],
MD [auth C],
ME [auth I],
MF [auth I],
MG [auth I],
MH [auth I],
MI [auth I],
NB [auth C],
NC [auth C],
ND [auth C],
NE [auth I],
NF [auth I],
NG [auth I],
NH [auth I],
NI [auth I],
OB [auth C],
OC [auth C],
OD [auth C],
OE [auth I],
OF [auth I],
OG [auth I],
OH [auth I],
PB [auth C],
PC [auth C],
PD [auth C],
PE [auth I],
PF [auth I],
PG [auth I],
PH [auth I],
PI [auth K],
QB [auth C],
QC [auth C],
QD [auth C],
QE [auth I],
QF [auth I],
QG [auth I],
QH [auth I],
QI [auth L],
RB [auth C],
RC [auth C],
RD [auth C],
RE [auth I],
RF [auth I],
RG [auth I],
RH [auth I],
SB [auth C],
SC [auth C],
SD [auth C],
SE [auth I],
SF [auth I],
SG [auth I],
SH [auth I],
SI [auth V],
TB [auth C],
TC [auth C],
TD [auth C],
TE [auth I],
TF [auth I],
TG [auth I],
TH [auth I],
UB [auth C],
UC [auth C],
UD [auth C],
UE [auth I],
UF [auth I],
UG [auth I],
UH [auth I],
VB [auth C],
VC [auth C],
VD [auth C],
VE [auth I],
VF [auth I],
VG [auth I],
VH [auth I],
WB [auth C],
WC [auth C],
WD [auth C],
WE [auth I],
WF [auth I],
WG [auth I],
WH [auth I],
XB [auth C],
XC [auth C],
XD [auth C],
XE [auth I],
XF [auth I],
XG [auth I],
XH [auth I],
YB [auth C],
YC [auth C],
YD [auth C],
YE [auth I],
YF [auth I],
YG [auth I],
YH [auth I],
ZB [auth C],
ZC [auth C],
ZD [auth C],
ZE [auth I],
ZF [auth I],
ZG [auth I],
ZH [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4D4
Query on 4D4
X [auth U]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEMv1.0.0-beta
MODEL REFINEMENTPHENIX1.19.2
MODEL REFINEMENTISOLDE1.2.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI137270
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI148120
Other governmentS10OD020054
Other governmentS10OD021741
Other governmentU24 GM129541
Other governmentU24 GM129539
Other governmentSimons Foundation (SF349247)
Other privateW.M. Keck Foundation Medical Research Grant
Other privateSangvhi-Agarwal Innovation Award
Other governmentNSF GRFP
Other privateUCSF Discovery Fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-03-02
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations