5TCU

Methicillin sensitive Staphylococcus aureus 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1128/mBio.00395-17
  • Primary Citation of Related Structures:  

  • 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 demonst ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
SB
202Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsC
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW12
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
SC
198Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsD
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXK6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
SD
156Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW23
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
SE
95Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q2G113 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G113
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
SG
155Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P48940 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P48940
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
SF
130Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsH
Find proteins for Q2FW20 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW20
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
SH
127Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsI
Find proteins for Q2FW39 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW39
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
S1
80Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q2YYP5 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
S2
114Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsK
Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW31
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
S3
136Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsL
Find proteins for P0A0H0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0H0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
S4
113Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsM
Find proteins for Q2FW30 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW30
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
S5
60Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsZ (rpsN1)
Find proteins for Q2FW19 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW19
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
S6
88Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G2Q1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
S7
83Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ45
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
S8
80Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW15
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
S9
56Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q2G111 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G111
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
SI
78Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW10
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
SA
79Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsT
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXY6
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
L2
274Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
LC
215Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
LJ
205Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
LK
166Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW18
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
LL
174Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW21
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
LM
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
LN
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
LO
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplO
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
LP
136Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
LQ
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
LR
113Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
L1
109Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
L3
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
L4
102Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
L5
112Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
L6
89Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
L7
103Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
L8
93Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0S0
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
L9
82Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
LA
58Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ60
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
LB
62Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
LD
57Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
LE
47Staphylococcus aureus (strain Mu3 / ATCC 700698)Mutation(s): 0 
Gene Names: rpmF
Find proteins for A7X145 (Staphylococcus aureus (strain Mu3 / ATCC 700698))
Go to UniProtKB:  A7X145
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 1
LS
47Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmG1
Find proteins for Q2FYU6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FYU6
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
LG
43Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
LH
60Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
LI
37Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW29
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
LF
74Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmE2
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FWD8
Entity ID: 1
MoleculeChainsLengthOrganism
16S RRNAA1555Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 20
MoleculeChainsLengthOrganism
mRNAX13Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 21
MoleculeChainsLengthOrganism
P-site tRNA CHAINE75Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 22
MoleculeChainsLengthOrganism
E-site tRNA CHAIND76Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 23
MoleculeChainsLengthOrganism
23S RRNAB2923Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 24
MoleculeChainsLengthOrganism
5S rRNA CHAINC114Staphylococcus aureus subsp. aureus NCTC 8325
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download SDF File 
Download CCD File 
A
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, SG
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia1092262
European Research CouncilIsrael322581 (NOVRIB)

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Data collection