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- EMDB-21908: 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBod... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21908 | |||||||||
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Title | 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement | |||||||||
![]() | 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement | |||||||||
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![]() | 70S / ribosome / pathogen / antibiotic development / antibiotic resistant | |||||||||
Function / homology | ![]() ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Jogl G / Khayat R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis. Authors: Eileen L Murphy / Kavindra V Singh / Bryant Avila / Torsten Kleffmann / Steven T Gregory / Barbara E Murray / Kurt L Krause / Reza Khayat / Gerwald Jogl / ![]() ![]() Abstract: Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ...Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 301.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.4 KB 21.4 KB | Display Display | ![]() |
Images | ![]() | 15 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 631 KB | Display | ![]() |
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Full document | ![]() | 630.6 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wuaMC ![]() 0656C ![]() 0657C ![]() 0658C ![]() 0659C ![]() 0660C ![]() 6o8wC ![]() 6o8xC ![]() 6o8yC ![]() 6o8zC ![]() 6o90C ![]() 6w6pC ![]() 6wu9C ![]() 6wubC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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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 | 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.097 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Enterococcus faecalis
+Supramolecule #1: Enterococcus faecalis
+Macromolecule #1: 16S rRNA
+Macromolecule #2: 30S ribosomal protein S3
+Macromolecule #3: 30S ribosomal protein S7
+Macromolecule #4: 30S ribosomal protein S9
+Macromolecule #5: 30S ribosomal protein S10
+Macromolecule #6: 30S ribosomal protein S13
+Macromolecule #7: 30S ribosomal protein S14 type Z
+Macromolecule #8: 30S ribosomal protein S19
+Macromolecule #9: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Vol = 4 uL, BT = 4 sec, BF = 0, DT = 0, WT = 8 sec. |
Details | Sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Ab initio |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.63) / Number images used: 335675 |
Initial angle assignment | Type: COMMON LINE / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 0.63) |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 177 / Target criteria: Correlation Coefficient | ||||||
Output model | ![]() PDB-6wua: |