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- EMDB-15864: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S... -

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Entry
Database: EMDB / ID: EMD-15864
TitleCryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
Map datapost-processed masked map
Sample
  • Complex: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
KeywordsRibosome / Listeria monocytogenes / Lincomycin / 50S / antibiotic
Biological speciesListeria monocytogenes E (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsKoller TO / Crowe-McAuliffe C / Wilson DN
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Other governmentDLR01KI1820
Swedish Research Council2018-00956 Sweden
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes.
Authors: Timm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C ...Authors: Timm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C Atkinson / Jörgen Johansson / Vasili Hauryliuk / Daniel N Wilson /
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 ...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.
History
DepositionSep 27, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15864.png

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Map

FileDownload / File: emd_15864.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed masked map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 400 pix.
= 309. Å		0.77 Å/pix.
x 400 pix.
= 309. Å		0.77 Å/pix.
x 400 pix.
= 309. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.18016164 - 0.43900388
Average (Standard dev.)0.0006593081 (±0.010668805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 309.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D refined map

Fileemd_15864_additional_1.map
Annotation3D refined map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: post-processed map

Fileemd_15864_additional_2.map
Annotationpost-processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map1

Fileemd_15864_half_map_1.map
Annotationhalf-map1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half-map2

Fileemd_15864_half_map_2.map
Annotationhalf-map2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S...

EntireName: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
Components
  • Complex: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.

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Supramolecule #1: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S...

SupramoleculeName: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#29
Source (natural)Organism: Listeria monocytogenes E (bacteria)
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
15.0 mMMg(OAc)2Magnesium acetate
95.0 mMKClPotassium chloride
5.0 mMNH4ClAmmonium chloride
0.5 mMCaCl2Calcium chloride
8.0 mMC4H12N2Putrescine
1.0 mMC7H19N3Spermidine
0.5 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid

Details: 0.05% Nikkol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details5 OD260/mL

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 270000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 506262
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7nhn


Details: Listeria monocytogenes 70S
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 6 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 285330
FSC plot (resolution estimation)

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