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Yorodumi- EMDB-27009: Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27009 | |||||||||
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Title | Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map | |||||||||
Map data | Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map | |||||||||
Sample |
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Function / homology | Function and homology information 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 / translation / ribonucleoprotein complex / mRNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Cutibacterium acnes (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
Authors | Lomakin IB / Devarkar SC / Bunick CG | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Authors: Ivan B Lomakin / Swapnil C Devarkar / Shivali Patel / Ayman Grada / Christopher G Bunick / Abstract: Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, ...Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome. #1: Journal: To Be Published Title: The structure of the Cutibacterium acnes 70S ribosome Authors: Lomakin IB / Devarkar SC / Grada A / Bunick CG | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27009.map.gz | 76.1 MB | EMDB map data format | |
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Header (meta data) | emd-27009-v30.xml emd-27009.xml | 47.1 KB 47.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27009_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_27009.png | 41.4 KB | ||
Others | emd_27009_half_map_1.map.gz emd_27009_half_map_2.map.gz | 139.3 MB 139.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27009 | HTTPS FTP |
-Validation report
Summary document | emd_27009_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_27009_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_27009_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | emd_27009_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27009 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27009 | HTTPS FTP |
-Related structure data
Related structure data | 8cvmMC 8crxC 8cvoC 8cwoC 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_27009.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cutibacterium acnes 50S ribosomal subunit with P-site tRNA...
File | emd_27009_half_map_1.map | ||||||||||||
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Annotation | Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cutibacterium acnes 50S ribosomal subunit with P-site tRNA...
File | emd_27009_half_map_2.map | ||||||||||||
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Annotation | Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 50S subunit from 70S ribosome with mRNA, P-site tRNA and Sarecycl...
+Supramolecule #1: 50S subunit from 70S ribosome with mRNA, P-site tRNA and Sarecycl...
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L13
+Macromolecule #7: 50S ribosomal protein L14
+Macromolecule #8: 50S ribosomal protein L15
+Macromolecule #9: 50S ribosomal protein L16
+Macromolecule #10: 50S ribosomal protein L17
+Macromolecule #11: 50S ribosomal protein L18
+Macromolecule #12: 50S ribosomal protein L19
+Macromolecule #13: 50S ribosomal protein L20
+Macromolecule #14: 50S ribosomal protein L21
+Macromolecule #15: 50S ribosomal protein L22
+Macromolecule #16: 50S ribosomal protein L23
+Macromolecule #17: 50S ribosomal protein L24
+Macromolecule #18: 50S ribosomal protein L25
+Macromolecule #19: 50S ribosomal protein L27
+Macromolecule #20: 50S ribosomal protein L28
+Macromolecule #21: 50S ribosomal protein L29
+Macromolecule #22: 50S ribosomal protein L30
+Macromolecule #23: 50S ribosomal protein L32
+Macromolecule #24: 50S ribosomal protein L33
+Macromolecule #25: 50S ribosomal protein L34
+Macromolecule #26: 50S ribosomal protein L35
+Macromolecule #27: 50S ribosomal protein L31
+Macromolecule #30: 50S ribosomal protein bL37
+Macromolecule #32: 50S ribosomal protein L36
+Macromolecule #28: 23S ribosomal RNA
+Macromolecule #29: 5S ribosomal RNA
+Macromolecule #31: Initiator fMet RNA
+Macromolecule #33: MAGNESIUM ION
+Macromolecule #34: ZINC ION
+Macromolecule #35: Sarecycline
+Macromolecule #36: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.1 sec. / Average electron dose: 30.56 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8cvm: |