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Yorodumi- EMDB-15161: Cryo-EM structure of HflXr bound to the Listeria monocytogenes 50... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15161 | |||||||||
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Title | Cryo-EM structure of HflXr bound to the Listeria monocytogenes 50S ribosomal subunit. | |||||||||
Map data | Post-processed masked map | |||||||||
Sample |
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Keywords | Ribosome / Listeria monocytogenes / HflXr / 50S / antibiotic resistance | |||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation ...large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes E (bacteria) / Listeria monocytogenes EGD-e (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Koller TO / Crowe-McAuliffe C / Wilson DN | |||||||||
Funding support | Germany, 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_15161.map.gz | 30.3 MB | EMDB map data format | |
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Header (meta data) | emd-15161-v30.xml emd-15161.xml | 58.1 KB 58.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15161_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_15161.png | 94 KB | ||
Filedesc metadata | emd-15161.cif.gz | 11.1 KB | ||
Others | emd_15161_additional_1.map.gz emd_15161_additional_2.map.gz emd_15161_half_map_1.map.gz emd_15161_half_map_2.map.gz | 26.1 MB 140.2 MB 140.9 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15161 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15161 | HTTPS FTP |
-Validation report
Summary document | emd_15161_validation.pdf.gz | 1009.6 KB | Display | EMDB validaton report |
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Full document | emd_15161_full_validation.pdf.gz | 1009.2 KB | Display | |
Data in XML | emd_15161_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_15161_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15161 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15161 | HTTPS FTP |
-Related structure data
Related structure data | 8a57MC 8a5iC 8a63C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15161.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Post-processed masked map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Post-processed masked map 3A lowpass filtered
File | emd_15161_additional_1.map | ||||||||||||
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Annotation | Post-processed masked map 3A lowpass filtered | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D refined map
File | emd_15161_additional_2.map | ||||||||||||
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Annotation | 3D refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_15161_half_map_1.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_15161_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : HflXr bound to the Listeria monocytogenes 50S ribosomal subunit
+Supramolecule #1: HflXr 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 #30: GTPase HflX
+Macromolecule #31: 50S ribosomal protein L11
+Macromolecule #10: 23S ribosomal RNA
+Macromolecule #11: 5S ribosomal RNA
+Macromolecule #32: ZINC ION
+Macromolecule #33: SPERMIDINE
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: 1,4-DIAMINOBUTANE
+Macromolecule #36: POTASSIUM ION
+Macromolecule #37: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-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 and 0.2 mg/mL FLAG peptide during elution. | |||||||||||||||||||||||||||
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||||||||
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: 35.022 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |