8A63

Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit.


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 1.2 of the entry. See complete history


Literature

Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes.

Koller, T.O.Turnbull, K.J.Vaitkevicius, K.Crowe-McAuliffe, C.Roghanian, M.Bulvas, O.Nakamoto, J.A.Kurata, T.Julius, C.Atkinson, G.C.Johansson, J.Hauryliuk, V.Wilson, D.N.

(2022) Nucleic Acids Res 50: 11285-11300

  • DOI: https://doi.org/10.1093/nar/gkac934
  • Primary Citation of Related Structures:  
    8A57, 8A5I, 8A63

  • PubMed Abstract: 

    HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers resistance to macrolide and lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. monocytogenes HflXr-50S and HflX-50S complexes as well as L. monocytogenes 70S ribosomes in the presence and absence of the lincosamide lincomycin. While the overall geometry of HflXr on the 50S subunit is similar to that of HflX, a loop within the N-terminal domain of HflXr, which is two amino acids longer than in HflX, reaches deeper into the peptidyltransferase center. Moreover, unlike HflX, the binding of HflXr induces conformational changes within adjacent rRNA nucleotides that would be incompatible with drug binding. These findings suggest that HflXr confers resistance using an allosteric ribosome protection mechanism, rather than by simply splitting and recycling antibiotic-stalled ribosomes.


  • 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
50S ribosomal protein L28A [auth 1]62Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for P66144 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29B [auth 2]63Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for P66166 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30C [auth 3]59Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BD [auth 4]81Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for P0A485 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32-2E [auth 5]57Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for P66207 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1F [auth 6]49Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34G [auth 7]44Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35H [auth 8]66Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36I [auth 9]37Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2L [auth G]277Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for P60426 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3M [auth H]209Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4N [auth I]207Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for P61055 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5O [auth J]179Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6P [auth K]178Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13Q [auth M]145Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14R [auth N]122Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for Q927L7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15S [auth O]146Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for Q8Y447 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16T [auth P]144Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17U [auth Q]135Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for Q8Y450 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18V [auth R]119Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19W [auth S]114Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
Find proteins for O53083 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20X [auth T]119Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Y [auth U]102Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Z [auth V]118Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23AA [auth W]94Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24BA [auth X]103Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CA [auth Z]96Listeria monocytogenes EGD-eMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S ribosomal RNAJ [auth A]2,931Listeria monocytogenes EGD-e
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Entity ID: 11
MoleculeChains LengthOrganismImage
5S ribosomal RNAK [auth B]114Listeria monocytogenes EGD-e
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

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FA [auth A]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT
Query on PUT

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AG [auth A],
ZF [auth A]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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DA [auth 5],
EA [auth 9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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QG [auth P]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [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],
DC [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],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth G],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth H],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth O],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentDLR01KI1820
Swedish Research CouncilSweden2018-00956

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references