5TCU

Methicillin sensitive Staphylococcus aureus 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome.

Belousoff, M.J.Eyal, Z.Radjainia, M.Ahmed, T.Bamert, R.S.Matzov, D.Bashan, A.Zimmerman, E.Mishra, S.Cameron, D.Elmlund, H.Peleg, A.Y.Bhushan, S.Lithgow, T.Yonath, A.

(2017) mBio 8

  • DOI: https://doi.org/10.1128/mBio.00395-17
  • Primary Citation of Related Structures:  
    5T7V, 5TCU

  • PubMed Abstract: 

    An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.


  • Organizational Affiliation

    Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, Australia.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth SB]202Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth SC]198Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth SD]156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth SE]95Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth SG]155Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth SF]130Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth SH]127Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth S1]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth S2]114Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth S3]136Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth S4]113Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZM [auth S5]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth S6]88Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth S7]83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth S8]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth S9]56Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth SI]78Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth SA]79Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth L2]274Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth LC]215Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth LJ]205Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth LK]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth LL]174Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth LM]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth LN]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth LO]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth LP]136Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth LQ]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18IA [auth LR]113Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth L1]109Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20KA [auth L3]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21LA [auth L4]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22MA [auth L5]112Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth L6]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24OA [auth L7]103Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25PA [auth L8]93Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth L9]82Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28RA [auth LA]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29SA [auth LB]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth LD]57Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UA [auth LE]47Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1VA [auth LS]47Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth LG]43Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupQ2FUQ0
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth LH]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth LI]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BZA [auth LF]74Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupQ2FWD8
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RRNA1,555Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 20
MoleculeChains LengthOrganismImage
mRNAT [auth X]13Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 21
MoleculeChains LengthOrganismImage
P-site tRNA CHAINU [auth E]75Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 22
MoleculeChains LengthOrganismImage
E-site tRNA CHAINV [auth D]76Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S RRNAW [auth B]2,923Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S rRNA CHAINX [auth C]114Staphylococcus aureus subsp. aureus NCTC 8325
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
AB [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth B]
AE [auth B]
AF [auth B]
BB [auth A]
AC [auth A],
AD [auth B],
AE [auth B],
AF [auth B],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth B],
BF [auth B],
CB [auth A],
CC [auth SG],
CD [auth B],
CE [auth B],
CF [auth B],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth B],
DF [auth B],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth B],
EF [auth B],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth B],
FF [auth B],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth B],
GF [auth B],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth B],
HF [auth B],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth B],
IF [auth B],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth B],
JF [auth B],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth B],
KF [auth B],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth B],
LF [auth B],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth B],
MF [auth B],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth B],
NF [auth B],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth B],
OF [auth B],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth B],
PF [auth B],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth B],
QF [auth B],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth B],
RF [auth B],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth B],
SF [auth B],
TB [auth A],
TC [auth B],
TD [auth B],
TE [auth B],
TF [auth B],
UB [auth A],
UC [auth B],
UD [auth B],
UE [auth B],
UF [auth B],
VB [auth A],
VC [auth B],
VD [auth B],
VE [auth B],
VF [auth B],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth B],
WF [auth B],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth B],
XF [auth B],
YB [auth A],
YC [auth B],
YD [auth B],
YE [auth B],
YF [auth C],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth B],
ZF [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1092262
European Research Council (ERC)European Union322581 (NOVRIB)

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-18
    Changes: Advisory, Author supporting evidence, Derived calculations, Other
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-10-30
    Changes: Data collection