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- EMDB-15670: Cryo-EM volume of HflX bound to the Listeria monocytogenes 50S ri... -

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Basic information

Entry
Database: EMDB / ID: EMD-15670
TitleCryo-EM volume of HflX bound to the Listeria monocytogenes 50S ribosomal subunit
Map datamasked post processed map
Sample
  • Complex: Masked post processed map of HflX bound to the 50S subunit of the Listeria monocytogenes ribosome.
KeywordsListeria monocytogenes / 50S / Ribosome / HflX / Antibiotic / Target protection / GTPase / GDPNP
Biological speciesListeria monocytogenes EGD-e (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsKoller TO / Crowe-McAuliffe C / Wilson DN
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other governmentDLR01Kl1820 Germany
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
DepositionAug 25, 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_15670.png

Downloads & links

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Map

FileDownload / File: emd_15670.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked post processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.1374938 - 0.17328663
Average (Standard dev.)0.00009356254 (±0.006772678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: masked post processed 3A lowpass filtered map

Fileemd_15670_additional_1.map
Annotationmasked post processed 3A lowpass filtered map
Projections & Slices
AxesZYX

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Additional map: post processed map

Fileemd_15670_additional_2.map
Annotationpost processed map
Projections & Slices
AxesZYX

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Histogram

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Additional map: 3D refined map

Fileemd_15670_additional_3.map
Annotation3D refined map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map 2

Fileemd_15670_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_15670_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Masked post processed map of HflX bound to the 50S subunit of the...

EntireName: Masked post processed map of HflX bound to the 50S subunit of the Listeria monocytogenes ribosome.
Components
  • Complex: Masked post processed map of HflX bound to the 50S subunit of the Listeria monocytogenes ribosome.

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Supramolecule #1: Masked post processed map of HflX bound to the 50S subunit of the...

SupramoleculeName: Masked post processed map of HflX bound to the 50S subunit of the Listeria monocytogenes ribosome.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 268147
Startup modelType of model: EMDB MAP
EMDB ID:

15175

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 76519
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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