7P7R

PoxtA-EQ2 antibiotic resistance ABCF bound to E. faecalis 70S ribosome, state I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics.

Crowe-McAuliffe, C.Murina, V.Turnbull, K.J.Huch, S.Kasari, M.Takada, H.Nersisyan, L.Sundsfjord, A.Hegstad, K.Atkinson, G.C.Pelechano, V.Wilson, D.N.Hauryliuk, V.

(2022) Nat Commun 13: 1860-1860

  • DOI: https://doi.org/10.1038/s41467-022-29274-9
  • Primary Citation of Related Structures:  
    7P7Q, 7P7R, 7P7S, 7P7T, 7P7U

  • PubMed Abstract: 

    PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall translating ribosomes when certain amino acids are present at a defined position in the nascent polypeptide chain. These proteins are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria, and are thought to confer resistance by binding to the ribosome and dislodging the bound antibiotic. However, the mechanistic basis of this resistance remains unclear. Here we refine the PoxtA spectrum of action, demonstrate alleviation of linezolid-induced context-dependent translational stalling, and present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome. PoxtA perturbs the CCA-end of the P-site tRNA, causing it to shift by ∼4 Å out of the ribosome, corresponding to a register shift of approximately one amino acid for an attached nascent polypeptide chain. We postulate that the perturbation of the P-site tRNA by PoxtA thereby alters the conformation of the attached nascent chain to disrupt the drug binding site.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ARE-ABC-F family resistance factor PoxtAA [auth 0]586Enterococcus faecalis V583Mutation(s): 0 
Gene Names: poxtA
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29B [auth 1]62Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30C [auth 2]59Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BD [auth 3]89Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32-3E [auth 4]59Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 3F [auth 5]48Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34G [auth 6]44Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35H [auth 7]65Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36I [auth 8]38Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1M [auth F]229Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2N [auth G]276Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3O [auth H]209Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4P [auth I]207Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5Q [auth J]179Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6R [auth K]178Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13S [auth M]147Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14T [auth N]122Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15U [auth O]146Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16V [auth P]144Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17W [auth Q]127Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18X [auth R]118Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Y [auth S]115Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Z [auth T]119Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21AA [auth U]102Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22BA [auth V]115Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23CA [auth W]96Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24DA [auth X]103Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27EA [auth Y]95Enterococcus faecalis V583Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28FA [auth Z]62Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth c]261Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth d]218Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth e]203Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth f]166Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth g]99Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth h]156Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth i]132Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth j]130Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth k]102Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth l]129Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth m]137Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth n]121Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZUA [auth o]61Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth p]89Enterococcus faecalis V583Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth q]91Enterococcus faecalis V583Mutation(s): 0 
UniProt
Find proteins for Q834F9 (Enterococcus faecalis (strain ATCC 700802 / V583))
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UniProt GroupQ834F9
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth r]88Enterococcus faecalis V583Mutation(s): 0 
UniProt
Find proteins for Q839F5 (Enterococcus faecalis (strain ATCC 700802 / V583))
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UniProt GroupQ839F5
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth s]79Enterococcus faecalis V583Mutation(s): 0 
UniProt
Find proteins for Q839Y8 (Enterococcus faecalis (strain ATCC 700802 / V583))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth t]92Enterococcus faecalis V583Mutation(s): 0 
UniProt
Find proteins for Q839G0 (Enterococcus faecalis (strain ATCC 700802 / V583))
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UniProt GroupQ839G0
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth u]83Enterococcus faecalis V583Mutation(s): 0 
UniProt
Find proteins for Q831Q7 (Enterococcus faecalis (strain ATCC 700802 / V583))
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S rRNAJ [auth A]2,912Enterococcus faecalis V583
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Entity ID: 11
MoleculeChains LengthOrganismImage
5S rRNAK [auth B]115Enterococcus faecalis V583
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Entity ID: 12
MoleculeChains LengthOrganismImage
tRNA-fMetL [auth D]77Enterococcus faecalis V583
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Entity ID: 33
MoleculeChains LengthOrganismImage
16S rRNAGA [auth a]1,558Enterococcus faecalis V583
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Entity ID: 34
MoleculeChains LengthOrganismImage
mRNAHA [auth b]19Enterococcus faecalis V583
Sequence Annotations
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BB [auth 0],
CB [auth 0]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SCM
Query on SCM

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YN [auth a]SPECTINOMYCIN
C14 H24 N2 O7
UNFWWIHTNXNPBV-WXKVUWSESA-N
PUT
Query on PUT

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NN [auth a]1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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FB [auth 4],
GB [auth 5],
JB [auth 8],
KO [auth o]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AL [auth P]
AM [auth a]
AN [auth a]
AC [auth A],
AD [auth A],
AL [auth P],
AM [auth a],
AN [auth a],
BC [auth A],
BD [auth A],
BH [auth A],
BM [auth a],
BN [auth a],
CC [auth A],
CD [auth A],
CL [auth a],
CM [auth a],
DC [auth A],
DD [auth A],
DI [auth A],
DJ [auth A],
DL [auth a],
DM [auth a],
DN [auth a],
EC [auth A],
ED [auth A],
EH [auth A],
EI [auth A],
EJ [auth A],
EL [auth a],
EM [auth a],
FC [auth A],
FD [auth A],
FH [auth A],
FL [auth a],
FO [auth a],
GC [auth A],
GD [auth A],
GJ [auth A],
GL [auth a],
GN [auth a],
GO [auth a],
HB [auth 7],
HC [auth A],
HD [auth A],
HJ [auth A],
HK [auth A],
HL [auth a],
HO [auth a],
IB [auth 7],
IC [auth A],
ID [auth A],
IF [auth A],
IJ [auth A],
IK [auth A],
IL [auth a],
IO [auth g],
JC [auth A],
JD [auth A],
JJ [auth A],
JK [auth A],
JL [auth a],
KC [auth A],
KD [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LG [auth A],
LI [auth A],
LK [auth A],
LL [auth a],
LO [auth o],
MB [auth A],
MC [auth A],
MD [auth A],
MG [auth A],
MK [auth A],
ML [auth a],
NB [auth A],
NC [auth A],
ND [auth A],
NK [auth A],
NL [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OK [auth A],
OL [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PK [auth A],
PL [auth a],
QB [auth A],
QC [auth A],
QD [auth A],
QK [auth A],
QL [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RK [auth A],
RL [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SL [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TH [auth A],
TK [auth B],
TL [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UK [auth B],
UL [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VK [auth B],
VL [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WH [auth A],
WL [auth a],
XB [auth A],
XC [auth A],
XD [auth A],
XH [auth A],
XK [auth G],
XL [auth a],
XN [auth a],
YB [auth A],
YC [auth A],
YH [auth A],
YK [auth G],
YL [auth a],
ZB [auth A],
ZC [auth A],
ZH [auth A],
ZK [auth G],
ZL [auth a],
ZM [auth a]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AE [auth A]
AF [auth A]
AG [auth A]
AH [auth A]
AI [auth A]
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AO [auth a],
BE [auth A],
BF [auth A],
BG [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth Q],
BO [auth a],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CN [auth a],
CO [auth a],
DB [auth 0],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
DK [auth A],
DO [auth a],
EB [auth 0],
EE [auth A],
EF [auth A],
EG [auth A],
EK [auth A],
EN [auth a],
EO [auth a],
FE [auth A],
FF [auth A],
FG [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
FM [auth a],
FN [auth a],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GK [auth A],
GM [auth a],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HM [auth a],
HN [auth a],
IE [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IM [auth a],
IN [auth a],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JM [auth a],
JN [auth a],
JO [auth n],
KB [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
KM [auth a],
KN [auth a],
LF [auth A],
LH [auth A],
LJ [auth A],
LM [auth a],
LN [auth a],
ME [auth A],
MF [auth A],
MH [auth A],
MI [auth A],
MJ [auth A],
MM [auth a],
MN [auth a],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth A],
NM [auth a],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OM [auth a],
ON [auth a],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PM [auth a],
PN [auth a],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QM [auth a],
QN [auth a],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RM [auth a],
RN [auth a],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth B],
SM [auth a],
SN [auth a],
TF [auth A],
TG [auth A],
TI [auth A],
TJ [auth A],
TM [auth a],
TN [auth a],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UM [auth a],
UN [auth a],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VM [auth a],
VN [auth a],
WE [auth A],
WF [auth A],
WG [auth A],
WI [auth A],
WJ [auth A],
WK [auth G],
WM [auth a],
WN [auth a],
XE [auth A],
XF [auth A],
XG [auth A],
XI [auth A],
XJ [auth A],
XM [auth a],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YI [auth A],
YJ [auth A],
YM [auth a],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZI [auth A],
ZJ [auth A],
ZN [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

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

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references, Structure summary
  • Version 1.2: 2024-07-17
    Changes: Data collection, Database references