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Yorodumi- EMDB-8937: Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8937 | ||||||||||||
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Title | Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit | ||||||||||||
Map data | Cryo-EM structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit | ||||||||||||
Sample |
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Keywords | Hibernation factor complex / RIBOSOME | ||||||||||||
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 / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||||||||
Authors | Sharma MR / Li Y / Korripella R / Yang Y / Kaushal PS / Lin Q / Wade JT / Gray AG / Derbyshire KM / Agrawal RK / Ojha A | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Zinc depletion induces ribosome hibernation in mycobacteria. Authors: Yunlong Li / Manjuli R Sharma / Ravi K Koripella / Yong Yang / Prem S Kaushal / Qishan Lin / Joseph T Wade / Todd A Gray / Keith M Derbyshire / Rajendra K Agrawal / Anil K Ojha / Abstract: Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc ...Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8937.map.gz | 18.2 MB | EMDB map data format | |
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Header (meta data) | emd-8937-v30.xml emd-8937.xml | 50.4 KB 50.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8937_fsc.xml | 15.7 KB | Display | FSC data file |
Images | emd_8937.png | 202.3 KB | ||
Filedesc metadata | emd-8937.cif.gz | 10.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8937 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8937 | HTTPS FTP |
-Validation report
Summary document | emd_8937_validation.pdf.gz | 434.9 KB | Display | EMDB validaton report |
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Full document | emd_8937_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | emd_8937_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_8937_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8937 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8937 | HTTPS FTP |
-Related structure data
Related structure data | 6dzpMC 8932C 8934C 6dziC 6dzkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8937.map.gz / Format: CCP4 / Size: 357 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Mycobacterium smegmatis C(minus) 70S ribosome with MPY
+Supramolecule #1: Mycobacterium smegmatis C(minus) 70S ribosome with MPY
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L9
+Macromolecule #9: 50S ribosomal protein L10
+Macromolecule #10: 50S ribosomal protein L11
+Macromolecule #11: 50S ribosomal protein L13
+Macromolecule #12: 50S ribosomal protein L14
+Macromolecule #13: 50S ribosomal protein L15
+Macromolecule #14: 50S ribosomal protein L16
+Macromolecule #15: 50S ribosomal protein L17
+Macromolecule #16: 50S ribosomal protein L18
+Macromolecule #17: 50S ribosomal protein L19
+Macromolecule #18: 50S ribosomal protein L20
+Macromolecule #19: 50S ribosomal protein L21
+Macromolecule #20: 50S ribosomal protein L22
+Macromolecule #21: 50S ribosomal protein L23
+Macromolecule #22: 50S ribosomal protein L24
+Macromolecule #23: 50S ribosomal protein L25
+Macromolecule #24: 50S ribosomal protein L27
+Macromolecule #25: 50S ribosomal protein L29
+Macromolecule #26: 50S ribosomal protein L30
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33 2
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #32: 50S ribosomal protein L31
+Macromolecule #33: 50S ribosomal protein L28
+Macromolecule #34: Uncharacterized protein
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Support film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I |
-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: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
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-6dzp: |