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- EMDB-38788: Mycobacterium smegmatis 50S ribosomal subunit with Erythromycin -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Mycobacterium smegmatis 50S ribosomal subunit with Erythromycin | |||||||||
![]() | Mycobacterium smegmatis 50S ribosomal subunit in complex with erythromycin | |||||||||
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![]() | Antibiotic / RIBOSOME | |||||||||
Function / homology | ![]() large ribosomal subunit / 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 ...large ribosomal subunit / 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 / mRNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Srinivasan K / Banerjee A / Sengupta J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria. Authors: Krishnamoorthi Srinivasan / Aneek Banerjee / Jayati Sengupta / ![]() Abstract: Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. ...Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. smegmatis (Msm) HflX-50S subunit and 50S subunit-erythromycin (ERY) complexes at a global resolution of approximately 3 Å. A conserved nucleotide A2286 at the gate of nascent peptide exit tunnel (NPET) adopts a swayed conformation in HflX-50S complex and interacts with a loop within the linker helical (LH) domain of MsmHflX that contains an additional 9 residues insertion. Interestingly, the swaying of this nucleotide, which is usually found in the non-swayed conformation, is induced by erythromycin binding. Furthermore, we observed that erythromycin decreases HflX's ribosome-dependent GTP hydrolysis, resulting in its enhanced binding and anti-association activity on the 50S subunit. Our findings reveal how mycobacterial HflX senses the presence of macrolides at the peptide tunnel entrance and confers antibiotic resistance in mycobacteria. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 255.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 54.4 KB 54.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.1 KB | Display | ![]() |
Images | ![]() | 96.2 KB | ||
Filedesc metadata | ![]() | 10.3 KB | ||
Others | ![]() ![]() | 225.2 MB 225.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1014 KB | Display | ![]() |
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Full document | ![]() | 1013.5 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xz3MC ![]() 8kabC M: atomic model generated by this map C: citing same article ( |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Mycobacterium smegmatis 50S ribosomal subunit in complex with erythromycin | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map of Mycobacterium smegmatis 50S ribosomal subunit in...
File | emd_38788_half_map_1.map | ||||||||||||
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Annotation | Half-map of Mycobacterium smegmatis 50S ribosomal subunit in complex with erythromycin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map of Mycobacterium smegmatis 50S ribosomal subunit in...
File | emd_38788_half_map_2.map | ||||||||||||
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Annotation | Half-map of Mycobacterium smegmatis 50S ribosomal subunit in complex with erythromycin | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Mycobacterium smegmatis 50S ribosomal subunit-erythromycin complex
+Supramolecule #1: Mycobacterium smegmatis 50S ribosomal subunit-erythromycin complex
+Supramolecule #2: Mycobacterium smegmatis 50S ribosomal subunit
+Macromolecule #1: 50S ribosomal protein bL37
+Macromolecule #4: Large ribosomal subunit protein uL2
+Macromolecule #5: Large ribosomal subunit protein uL3
+Macromolecule #6: Large ribosomal subunit protein uL4
+Macromolecule #7: Large ribosomal subunit protein uL5
+Macromolecule #8: Large ribosomal subunit protein uL6
+Macromolecule #9: 50S ribosomal protein L9
+Macromolecule #10: Large ribosomal subunit protein uL10
+Macromolecule #11: Large ribosomal subunit protein uL11
+Macromolecule #12: Large ribosomal subunit protein uL13
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: Large ribosomal subunit protein uL15
+Macromolecule #15: Large ribosomal subunit protein uL16
+Macromolecule #16: Large ribosomal subunit protein bL17
+Macromolecule #17: Large ribosomal subunit protein uL18
+Macromolecule #18: 50S ribosomal protein L19
+Macromolecule #19: Large ribosomal subunit protein bL20
+Macromolecule #20: Large ribosomal subunit protein bL21
+Macromolecule #21: Large ribosomal subunit protein uL22
+Macromolecule #22: Large ribosomal subunit protein uL23
+Macromolecule #23: Large ribosomal subunit protein uL24
+Macromolecule #24: Large ribosomal subunit protein bL25
+Macromolecule #25: Large ribosomal subunit protein bL27
+Macromolecule #26: Large ribosomal subunit protein bL28
+Macromolecule #27: Large ribosomal subunit protein uL29
+Macromolecule #28: Large ribosomal subunit protein uL30
+Macromolecule #29: Large ribosomal subunit protein bL32
+Macromolecule #30: Large ribosomal subunit protein bL33A
+Macromolecule #31: Large ribosomal subunit protein bL34
+Macromolecule #32: Large ribosomal subunit protein bL35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #34: Large ribosomal subunit protein bL31
+Macromolecule #2: 23S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #35: ERYTHROMYCIN A
-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 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 28.75 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |