8BUU

ARE-ABCF VmlR2 bound to a 70S ribosome


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

Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR.

Obana, N.Takada, H.Crowe-McAuliffe, C.Iwamoto, M.Egorov, A.A.Wu, K.J.Y.Chiba, S.Murina, V.Paternoga, H.Tresco, B.I.C.Nomura, N.Myers, A.G.Atkinson, G.C.Wilson, D.N.Hauryliuk, V.

(2023) Nucleic Acids Res 51: 4536-4554

  • DOI: https://doi.org/10.1093/nar/gkad193
  • Primary Citation of Related Structures:  
    8BUU

  • PubMed Abstract: 

    Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.


  • Organizational Affiliation

    Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth J]145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth K]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth L]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth M]144Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth N]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth O]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth P]115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth Q]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth R]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth S]113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth T]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth U]103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth W]94Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth X]62Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth Y]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth Z]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2Y [auth b]246Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 0]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1BA [auth 1]49Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 2]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth 3]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth 4]37Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6FA [auth f]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16GA [auth p]90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18HA [auth r]79Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20IA [auth t]88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4JA [auth d]200Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5KA [auth e]166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth h]132Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11NA [auth k]131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12OA [auth l]138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15PA [auth o]89Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17QA [auth q]87Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3RA [auth c]218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7SA [auth g]156Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9TA [auth i]130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10UA [auth j]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13VA [auth m]121Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14WA [auth n]61Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth s]92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P21476 (Bacillus subtilis (strain 168))
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Go to UniProtKB:  P21476
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UniProt GroupP21476
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
ExpZYA [auth 9]622Neobacillus viretiMutation(s): 2 
Gene Names: BAVI_03309
UniProt
Find proteins for W1SM44 (Neobacillus vireti LMG 21834)
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UniProt GroupW1SM44
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNA2,927Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNA119Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 20
MoleculeChains LengthOrganismImage
tRNA-fMetT [auth V]77Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 26
MoleculeChains LengthOrganismImage
mRNAZ [auth u]15Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 39
MoleculeChains LengthOrganismImage
16S rRNAMA [auth a]1,554Bacillus subtilis subsp. subtilis str. 168
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
YE [auth 9],
ZE [auth 9]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
TE [auth 0],
UE [auth 1],
VE [auth 4],
XE [auth n]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth A]
BB [auth A]
CB [auth A]
HE [auth A]
IE [auth A]
AB [auth A],
BB [auth A],
CB [auth A],
HE [auth A],
IE [auth A],
JE [auth A],
KE [auth A],
LE [auth A],
ME [auth A],
NE [auth A],
OE [auth A],
PE [auth A],
QE [auth A],
SE [auth U],
WE [auth a],
ZA [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 9]
BC [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth 9],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth 9],
CC [auth A],
CD [auth A],
CE [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth C],
SB [auth A],
SC [auth A],
SD [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZB [auth A],
ZC [auth A],
ZD [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
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWI3285/8-1
Swedish Research CouncilSweden2021-01146

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection