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- EMDB-15175: Cryo-EM structure of Lincomycin bound to the Listeria monocytogen... -
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Open data
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Basic information
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Title | Cryo-EM structure of Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit. | |||||||||
![]() | Post-processed masked final map. | |||||||||
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![]() | Ribosome / Listeria monocytogenes / Lincomycin / 50S / antibiotic | |||||||||
Function / homology | ![]() large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Koller TO / Crowe-McAuliffe C / Wilson DN | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 50.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 54.1 KB 54.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 88.7 KB | ||
Filedesc metadata | ![]() | 10.6 KB | ||
Others | ![]() ![]() ![]() | 194.6 MB 195.3 MB 195.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a5iMC ![]() 8a57C ![]() 8a63C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Post-processed masked final map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: Final 3D refined map.
File | emd_15175_additional_1.map | ||||||||||||
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Annotation | Final 3D refined map. | ||||||||||||
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Density Histograms |
-Half map: Half-map2.
File | emd_15175_half_map_1.map | ||||||||||||
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Annotation | Half-map2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1.
File | emd_15175_half_map_2.map | ||||||||||||
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Annotation | Half-map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
+Supramolecule #1: Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.
+Macromolecule #1: 50S ribosomal protein L28
+Macromolecule #2: 50S ribosomal protein L29
+Macromolecule #3: 50S ribosomal protein L30
+Macromolecule #4: 50S ribosomal protein L31 type B
+Macromolecule #5: 50S ribosomal protein L32-2
+Macromolecule #6: 50S ribosomal protein L33 1
+Macromolecule #7: 50S ribosomal protein L34
+Macromolecule #8: 50S ribosomal protein L35
+Macromolecule #9: 50S ribosomal protein L36
+Macromolecule #12: 50S ribosomal protein L2
+Macromolecule #13: 50S ribosomal protein L3
+Macromolecule #14: 50S ribosomal protein L4
+Macromolecule #15: 50S ribosomal protein L5
+Macromolecule #16: 50S ribosomal protein L6
+Macromolecule #17: 50S ribosomal protein L13
+Macromolecule #18: 50S ribosomal protein L14
+Macromolecule #19: 50S ribosomal protein L15
+Macromolecule #20: 50S ribosomal protein L16
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: 50S ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L27
+Macromolecule #10: 23S ribosomal RNA
+Macromolecule #11: 5S ribosomal RNA
+Macromolecule #30: ZINC ION
+Macromolecule #31: SPERMIDINE
+Macromolecule #32: MAGNESIUM ION
+Macromolecule #33: 1,4-DIAMINOBUTANE
+Macromolecule #34: LINCOMYCIN
+Macromolecule #35: POTASSIUM ION
+Macromolecule #36: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |