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- EMDB-0658: Cryo-EM image reconstruction of the 70S Ribosome Enterococcus fae... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0658 | |||||||||
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Title | Cryo-EM image reconstruction of the 70S Ribosome Enterococcus faecalis Class03 | |||||||||
![]() | 70S Ribosome Enterococcus faecalis Class03 | |||||||||
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![]() | 70S / ribosome / pathogen / antibiotic development / antibiotic resistant | |||||||||
Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.14 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 305.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 62.6 KB 62.6 KB | Display Display | ![]() |
Images | ![]() | 88.5 KB | ||
Filedesc metadata | ![]() | 12.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o8yMC ![]() 0656C ![]() 0657C ![]() 0659C ![]() 0660C ![]() 6o8wC ![]() 6o8xC ![]() 6o8zC ![]() 6o90C ![]() 6w6pC ![]() 6wu9C ![]() 6wuaC ![]() 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 | 70S Ribosome Enterococcus faecalis Class03 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 #20: 23S rRNA
+Macromolecule #21: 5S rRNA
+Macromolecule #2: 30S ribosomal protein S3
+Macromolecule #3: 30S ribosomal protein S4
+Macromolecule #4: 30S ribosomal protein S5
+Macromolecule #5: 30S ribosomal protein S6
+Macromolecule #6: 30S ribosomal protein S7
+Macromolecule #7: 30S ribosomal protein S8
+Macromolecule #8: 30S ribosomal protein S9
+Macromolecule #9: 30S ribosomal protein S10
+Macromolecule #10: 30S ribosomal protein S11
+Macromolecule #11: 30S ribosomal protein S12
+Macromolecule #12: 30S ribosomal protein S13
+Macromolecule #13: 30S ribosomal protein S14 type Z
+Macromolecule #14: 30S ribosomal protein S15
+Macromolecule #15: 30S ribosomal protein S16
+Macromolecule #16: 30S ribosomal protein S17
+Macromolecule #17: 30S ribosomal protein S18
+Macromolecule #18: 30S ribosomal protein S19
+Macromolecule #19: 30S ribosomal protein S20
+Macromolecule #22: 50S ribosomal protein L2
+Macromolecule #23: 50S ribosomal protein L3
+Macromolecule #24: 50S ribosomal protein L4
+Macromolecule #25: 50S ribosomal protein L5
+Macromolecule #26: 50S ribosomal protein L6
+Macromolecule #27: 50S ribosomal protein L13
+Macromolecule #28: 50S ribosomal protein L14
+Macromolecule #29: 50S ribosomal protein L15
+Macromolecule #30: 50S ribosomal protein L16
+Macromolecule #31: 50S ribosomal protein L17
+Macromolecule #32: 50S ribosomal protein L18
+Macromolecule #33: 50S ribosomal protein L19
+Macromolecule #34: 50S ribosomal protein L20
+Macromolecule #35: 50S ribosomal protein L21
+Macromolecule #36: 50S ribosomal protein L22
+Macromolecule #37: 50S ribosomal protein L23
+Macromolecule #38: 50S ribosomal protein L24
+Macromolecule #39: 50S ribosomal protein L25
+Macromolecule #40: 50S ribosomal protein L27
+Macromolecule #41: 50S ribosomal protein L28
+Macromolecule #42: 50S ribosomal protein L29
+Macromolecule #43: 50S ribosomal protein L30
+Macromolecule #44: 50S ribosomal protein L31 type B
+Macromolecule #45: 50S ribosomal protein L32
+Macromolecule #46: 50S ribosomal protein L33
+Macromolecule #47: 50S ribosomal protein L34
+Macromolecule #48: 50S ribosomal protein L35
+Macromolecule #49: 50S ribosomal protein L36
+Macromolecule #50: 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 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 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: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.63) / Number images used: 18979 |
Initial angle assignment | Type: COMMON LINE / Software - Name: RELION (ver. 2) |
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-6o8y: |