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Yorodumi- PDB-8fn2: The structure of a 50S ribosomal subunit in the Lyme disease path... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fn2 | ||||||
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Title | The structure of a 50S ribosomal subunit in the Lyme disease pathogen Borreliella burgdorferi | ||||||
Components |
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Keywords | RIBOSOME / hibernating ribosome / bacterial / pathogen / 50S / translation | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Borreliella burgdorferi B31 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Sharma, M.R. / Manjari, S.R. / Agrawal, E.K. / Keshavan, P. / Koripella, R.K. / Majumdar, S. / Marcinkiewicz, A.L. / Lin, Y.P. / Agrawal, R.K. / Banavali, N.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The structure of a hibernating ribosome in a Lyme disease pathogen. Authors: Manjuli R Sharma / Swati R Manjari / Ekansh K Agrawal / Pooja Keshavan / Ravi K Koripella / Soneya Majumdar / Ashley L Marcinkiewicz / Yi-Pin Lin / Rajendra K Agrawal / Nilesh K Banavali / Abstract: The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. ...The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. Here we present the structure of the Bbu 70S ribosome obtained by single particle cryo-electron microscopy at 2.9 Å resolution, revealing a bound hibernation promotion factor protein and two genetically non-annotated ribosomal proteins bS22 and bL38. The ribosomal protein uL30 in Bbu has an N-terminal α-helical extension, partly resembling the mycobacterial bL37 protein, suggesting evolution of bL37 and a shorter uL30 from a longer uL30 protein. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energy predictions for antibiotics reflect subtle distinctions in antibiotic-binding sites in the Bbu ribosome. Discovery of these features in the Bbu ribosome may enable better ribosome-targeted antibiotic design for Lyme disease treatment. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fn2.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fn2.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8fn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fn2_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8fn2_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8fn2_validation.xml.gz | 155.9 KB | Display | |
Data in CIF | 8fn2_validation.cif.gz | 257.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/8fn2 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/8fn2 | HTTPS FTP |
-Related structure data
Related structure data | 29304MC 8fmwC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 948648.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: GenBank: AE000783 |
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#2: RNA chain | Mass: 36188.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: GenBank: AE000783 |
+50S ribosomal protein ... , 32 types, 32 molecules DEFGHIJKLMNOPQRSTUVWXYZabcdefghi
-Non-polymers , 1 types, 2 molecules
#35: Chemical |
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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: 50S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Borreliella burgdorferi (Lyme disease spirochete) / Strain: B31 | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: HMA-10 buffer | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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 / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 820 nm / Cs: 0.001 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 67.527 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4661 |
EM imaging optics | Energyfilter slit width: 30 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 541319 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12449 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 2 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient |