7NHM

70S ribosome from Staphylococcus aureus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.

Crowe-McAuliffe, C.Murina, V.Turnbull, K.J.Kasari, M.Mohamad, M.Polte, C.Takada, H.Vaitkevicius, K.Johansson, J.Ignatova, Z.Atkinson, G.C.O'Neill, A.J.Hauryliuk, V.Wilson, D.N.

(2021) Nat Commun 12: 3577-3577

  • DOI: https://doi.org/10.1038/s41467-021-23753-1
  • Primary Citation of Related Structures:  
    7NHK, 7NHL, 7NHM, 7NHN

  • PubMed Abstract: 

    Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaA LC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27A [auth Z]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16B [auth P]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2F [auth G]277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth H]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4H [auth I]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5I [auth J]179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6J [auth K]178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth M]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth N]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth O]146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth Q]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth R]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth S]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth T]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth U]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth V]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth W]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth X]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P60735 (Staphylococcus aureus (strain N315))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth Y]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth 1]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth 2]69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P66173 (Staphylococcus aureus (strain N315))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth 3]59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth 5]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 2AA [auth 6]49Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BA [auth 8]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 7]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3DA [auth d]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4EA [auth e]200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7FA [auth h]156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10GA [auth k]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for A0A0D1JTN2 (Staphylococcus aureus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11HA [auth l]129Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZIA [auth o]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15JA [auth p]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16KA [auth q]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20LA [auth u]83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36MA [auth 9]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19NA [auth t]92Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13OA [auth n]121Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth j]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5QA [auth f]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8RA [auth i]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18SA [auth s]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6TA [auth g]98Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12VA [auth m]137Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P0A0H0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupP0A0H0
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17WA [auth r]87Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupQ2FW15
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2XA [auth c]255Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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UniProt GroupQ2FZ25
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BZA [auth 4]84Staphylococcus 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: 3
MoleculeChains LengthOrganismImage
23S rRNAC [auth A]2,923Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 4
MoleculeChains LengthOrganismImage
16S rRNAD [auth a]1,551Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAE [auth B]115Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 47
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*GP*AP*GP*GP*UP*NP*NP*NP*NP*NP*NP*AP*UP*G)-3')UA [auth b]15Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 51
MoleculeChains LengthOrganismImage
tRNA-fMetYA [auth D]77Staphylococcus aureus subsp. aureus NCTC 8325
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download Ideal Coordinates CCD File 
AH [auth D]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
ZN
Query on ZN

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VG [auth 5],
WG [auth 6],
XG [auth o],
YG [auth 9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth A]
DC [auth A]
IE [auth A]
MD [auth A]
NB [auth A]
AB [auth A],
DC [auth A],
IE [auth A],
MD [auth A],
NB [auth A],
SE [auth A],
TD [auth A],
VF [auth a],
WB [auth A],
WF [auth a],
YE [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth a]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth a],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth a],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth a],
DB [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth a],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth a],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth a],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IF [auth A],
IG [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth a],
MB [auth A],
MC [auth A],
ME [auth A],
MF [auth A],
MG [auth a],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth a],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SF [auth A],
SG [auth a],
TB [auth A],
TC [auth A],
TE [auth A],
TF [auth a],
TG [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth a],
UG [auth U],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth a],
YB [auth A],
YC [auth A],
YD [auth A],
YF [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth a],
ZG [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWI3285/8-1
Swedish Research CouncilSweden2017-03783
Swedish Research CouncilSweden2019-01085
European Regional Development FundSweden2014-2020.4.01.15-0013
Estonian Research CouncilEstoniaPRG335
Swedish Research CouncilSweden2018-00956

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references