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Yorodumi- EMDB-15864: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15864 | |||||||||
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Title | Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit. | |||||||||
Map data | post-processed masked map | |||||||||
Sample |
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Keywords | Ribosome / Listeria monocytogenes / Lincomycin / 50S / antibiotic | |||||||||
Biological species | Listeria monocytogenes E (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Koller TO / Crowe-McAuliffe C / Wilson DN | |||||||||
Funding support | Sweden, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15864.map.gz | 33.5 MB | EMDB map data format | |
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Header (meta data) | emd-15864-v30.xml emd-15864.xml | 26.1 KB 26.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15864_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_15864.png | 89.6 KB | ||
Filedesc metadata | emd-15864.cif.gz | 4.7 KB | ||
Others | emd_15864_additional_1.map.gz emd_15864_additional_2.map.gz emd_15864_half_map_1.map.gz emd_15864_half_map_2.map.gz | 193.2 MB 223.3 MB 193.6 MB 193.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15864 | HTTPS FTP |
-Validation report
Summary document | emd_15864_validation.pdf.gz | 941.8 KB | Display | EMDB validaton report |
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Full document | emd_15864_full_validation.pdf.gz | 941.4 KB | Display | |
Data in XML | emd_15864_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_15864_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15864 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15864.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | post-processed masked map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.7725 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: 3D refined map
File | emd_15864_additional_1.map | ||||||||||||
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Annotation | 3D refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post-processed map
File | emd_15864_additional_2.map | ||||||||||||
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Annotation | post-processed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map1
File | emd_15864_half_map_1.map | ||||||||||||
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Annotation | half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map2
File | emd_15864_half_map_2.map | ||||||||||||
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Annotation | half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S...
Entire | Name: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit. |
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Components |
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-Supramolecule #1: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S...
Supramolecule | Name: Cryo-EM map of lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#29 |
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Source (natural) | Organism: Listeria monocytogenes E (bacteria) |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 0.05% Nikkol | |||||||||||||||||||||||||||
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||||||||
Details | 5 OD260/mL |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 270000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |