5T7V

Methicillin Resistant, Linezolid resistant Staphylococcus aureus 70S ribosome (delta S145 uL3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Linezolid Binding Site Rearrangement in theStaphylococcus aureusRibosome.

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 S10
S1
82Staphylococcus aureusMutation(s): 0 
Gene Names: rpsJ (rpsJ_1)
Find proteins for A0A0H2K0A0 (Staphylococcus aureus)
Go to UniProtKB:  A0A0H2K0A0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
S2
115Staphylococcus aureusMutation(s): 0 
Gene Names: rpsK (rpsK_1, rpsK_2)
Find proteins for A0A077UKD6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKD6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
S3
136Staphylococcus aureusMutation(s): 0 
Gene Names: rpsL
Find proteins for W8U1C6 (Staphylococcus aureus)
Go to UniProtKB:  W8U1C6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
S6
87Staphylococcus aureusMutation(s): 0 
Gene Names: rpsO (rpsO_1)
Find proteins for W8U6H8 (Staphylococcus aureus)
Go to UniProtKB:  W8U6H8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
S7
76N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
S8
82Staphylococcus aureusMutation(s): 0 
Gene Names: rpsQ (rpsQ_1)
Find proteins for A0A077VLD5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VLD5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
S9
55N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
SA
76N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
SC
198Staphylococcus aureusMutation(s): 0 
Gene Names: rpsD (rpsD_2)
Find proteins for W8TVK2 (Staphylococcus aureus)
Go to UniProtKB:  W8TVK2
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
SD
154Staphylococcus aureusMutation(s): 0 
Gene Names: rpsE (rpsE_1)
Find proteins for W8TUC9 (Staphylococcus aureus)
Go to UniProtKB:  W8TUC9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
SE
92Staphylococcus aureusMutation(s): 0 
Gene Names: rpsF (rpsF_1, rpsF_2, rpsF_3, rpsF_4)
Find proteins for W8TPC6 (Staphylococcus aureus)
Go to UniProtKB:  W8TPC6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
SF
130Staphylococcus aureusMutation(s): 0 
Gene Names: rpsH (rpsH_1)
Find proteins for W8U8T8 (Staphylococcus aureus)
Go to UniProtKB:  W8U8T8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
L1
113Staphylococcus aureusMutation(s): 0 
Gene Names: rplS (rplS_1, rplS_2)
Find proteins for A0A077UVB6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UVB6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
L2
275Staphylococcus aureusMutation(s): 0 
Gene Names: rap (rplB)
Find proteins for B3VKN3 (Staphylococcus aureus)
Go to UniProtKB:  B3VKN3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
L3
116Staphylococcus aureusMutation(s): 0 
Gene Names: rplT (rplT_2)
Find proteins for A0A077VMP6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VMP6
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
L4
100Staphylococcus aureusMutation(s): 0 
Gene Names: rplU (rplU_1)
Find proteins for D7URR3 (Staphylococcus aureus)
Go to UniProtKB:  D7URR3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
L5
111Staphylococcus aureusMutation(s): 0 
Gene Names: rplV (rplV_1)
Find proteins for A0A077UKF9 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKF9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
L6
87Staphylococcus aureusMutation(s): 0 
Gene Names: rplW (rplW_1)
Find proteins for W8TUB4 (Staphylococcus aureus)
Go to UniProtKB:  W8TUB4
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
L7
101Staphylococcus aureusMutation(s): 0 
Gene Names: rplX (rplX_1)
Find proteins for W8TRD5 (Staphylococcus aureus)
Go to UniProtKB:  W8TRD5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
L8
93N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
L9
78N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
LA
59Staphylococcus aureusMutation(s): 0 
Gene Names: rpmB (rpmB_1)
Find proteins for A0A077URJ8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077URJ8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
LB
61Staphylococcus aureusMutation(s): 0 
Gene Names: rpmC (rpmC_1)
Find proteins for A0A077W1J5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077W1J5
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
LC
214Staphylococcus aureusMutation(s): 0 
Gene Names: rplC (rplC_1)
Find proteins for W8U3W0 (Staphylococcus aureus)
Go to UniProtKB:  W8U3W0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
LD
57Staphylococcus aureusMutation(s): 0 
Gene Names: rpmD (rpmD_1)
Find proteins for W8UVN7 (Staphylococcus aureus)
Go to UniProtKB:  W8UVN7
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
LE
53Staphylococcus aureusMutation(s): 0 
Gene Names: rpmF
Find proteins for A0A1Q8DAT0 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q8DAT0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
LF
47Staphylococcus aureusMutation(s): 0 
Gene Names: rpmG (rpmG_2)
Find proteins for A0A077UXT4 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UXT4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
LG
44Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2YZB6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YZB6
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
LH
64Staphylococcus aureusMutation(s): 0 
Gene Names: rpmI (rpmI_2)
Find proteins for A0A077UL47 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UL47
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
LI
37Staphylococcus aureusMutation(s): 0 
Gene Names: rpmJ (rpmJ_1)
Find proteins for A0A077UGV8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGV8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
LJ
204Staphylococcus aureusMutation(s): 0 
Gene Names: rplD (rplD_1)
Find proteins for W8TRC7 (Staphylococcus aureus)
Go to UniProtKB:  W8TRC7
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
LL
174Staphylococcus aureusMutation(s): 0 
Gene Names: rplF
Find proteins for A0A0U1MRH3 (Staphylococcus aureus)
Go to UniProtKB:  A0A0U1MRH3
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
LM
143Staphylococcus aureusMutation(s): 0 
Gene Names: rplM (rplM_1, rplM_2, rplM_3, rplM_4)
Find proteins for W8TUE6 (Staphylococcus aureus)
Go to UniProtKB:  W8TUE6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
LN
121Staphylococcus aureusMutation(s): 0 
Gene Names: rplN (rplN_1, rplNA)
Find proteins for A0A077UUA0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UUA0
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
LO
144Staphylococcus aureusMutation(s): 0 
Gene Names: rplO (rplO_1)
Find proteins for A0A077UGA7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGA7
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
LP
136Staphylococcus aureusMutation(s): 0 
Gene Names: rplP (rplP_1)
Find proteins for A0A077V4G0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V4G0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
LQ
121Staphylococcus aureusMutation(s): 0 
Gene Names: rplQ (rplQ_1, rplQ_2)
Find proteins for A0A077UG91 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UG91
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
LR
116Staphylococcus aureusMutation(s): 0 
Gene Names: rplR (rplR_1)
Find proteins for W8TRE0 (Staphylococcus aureus)
Go to UniProtKB:  W8TRE0
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1547Staphylococcus aureus
Entity ID: 14
MoleculeChainsLengthOrganism
23S ribosomal RNAB2919Staphylococcus aureus
Entity ID: 15
MoleculeChainsLengthOrganism
5S ribosomal RNAC114Staphylococcus aureus
Entity ID: 42
MoleculeChainsLengthOrganism
E-site tRNAD74Staphylococcus aureus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 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
NHMRCAustralia1092262

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection, Experimental preparation
  • Version 1.2: 2018-02-21
    Type: Database references
  • Version 1.3: 2018-03-28
    Type: Data collection, Database references