+Open data
-Basic information
Entry | Database: PDB / ID: 6w6p | |||||||||
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Title | MultiBody Refinement of 70S Ribosome from Enterococcus faecalis | |||||||||
Components |
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Keywords | RIBOSOME / 70S / pathogen / antibiotic development / antibiotic resistant | |||||||||
Function / homology | Function and homology information ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Enterococcus faecalis OG1RF (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Jogl, G. / Khayat, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6w6p.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6w6p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6w6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w6p_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6w6p_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6w6p_validation.xml.gz | 180.3 KB | Display | |
Data in CIF | 6w6p_validation.cif.gz | 324.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/6w6p ftp://data.pdbj.org/pub/pdb/validation_reports/w6/6w6p | HTTPS FTP |
-Related structure data
Related structure data | 21562MC 0656C 0657C 0658C 0659C 0660C 6o8wC 6o8xC 6o8yC 6o8zC 6o90C 6wu9C 6wuaC 6wubC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules aAB
#1: RNA chain | Mass: 501090.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853 |
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#20: RNA chain | Mass: 942675.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853 |
#21: RNA chain | Mass: 37433.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853 |
-30S ribosomal protein ... , 18 types, 18 molecules cdefghijklmnopqrst
#2: Protein | Mass: 22884.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR8 |
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#3: Protein | Mass: 23029.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRV7 |
#4: Protein | Mass: 17156.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKW0 |
#5: Protein | Mass: 11331.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKB6 |
#6: Protein | Mass: 17547.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKQ3 |
#7: Protein | Mass: 14805.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS6 |
#8: Protein | Mass: 14069.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XSA2 |
#9: Protein | Mass: 11400.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKR5 |
#10: Protein | Mass: 12322.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKV1 |
#11: Protein | Mass: 15178.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKQ7 |
#12: Protein | Mass: 12619.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT7 |
#13: Protein | Mass: 7041.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKT0 |
#14: Protein | Mass: 10537.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRW3 |
#15: Protein | Mass: 10095.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XP69 |
#16: Protein | Mass: 9744.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS3 |
#17: Protein | Mass: 7646.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKB3 |
#18: Protein | Mass: 8999.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A449DXS1 |
#19: Protein | Mass: 8841.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XQJ7 |
+50S ribosomal protein ... , 26 types, 26 molecules CDEFGKLMNOPQRSTUVXYZ023456
-Non-polymers , 1 types, 4 molecules
#48: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 70S ribosome / Type: RIBOSOME / Entity ID: #1-#47 / Source: NATURAL |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Source (natural) | Organism: Enterococcus faecalis OG1RF (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse. |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Vol = 4 uL, BT = 4 sec, BF = 0, DT = 0, WT = 8 sec |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335675 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 177 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation Coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.14 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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