Ribosomal protein L25, short-form / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. ...Ribosomal protein L25, short-form / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L27 / 50S ribosomal protein L6 / : / : ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L27 / 50S ribosomal protein L6 / : / : / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL2 / 50S ribosomal protein L33 / Large ribosomal subunit protein bL34 / 50S ribosomal protein L16 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L14 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L18 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / Large ribosomal subunit protein uL29 / 50S ribosomal protein L5 / 50S ribosomal protein L23 / 50S ribosomal protein L19 / 50S ribosomal protein L30 / 50S ribosomal protein L35 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L28 / 50S ribosomal protein L24 / Large ribosomal subunit protein bL32 / 50S ribosomal protein L20 Similarity search - Component
Biological species
Escherichia coli (E. coli)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI137270
United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
1R01GM127673-01
United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)
5P50GM082545-12
United States
Citation
Journal: Nucleic Acids Res / Year: 2020 Title: Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit. Authors: Vanja Stojković / Alexander G Myasnikov / Iris D Young / Adam Frost / James S Fraser / Danica Galonić Fujimori / Abstract: Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been ...Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.
History
Deposition
Jun 27, 2019
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Jan 22, 2020
Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0
Jan 22, 2020
Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update
Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 50S ribosomal subunit was purified from E. coli MRE600 using modified version of previously published protocol (Mehta et al. 2012)
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 10 K Details: Blot Force 5 Blot Time 10sec Hum 95% Temperature 10C Waiting time 1 min
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Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 130 K / Temperature (min): 86 K / Residual tilt: 10 mradians
Image recording
Average exposure time: 8 sec. / Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1889
Image scans
Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 80 / Used frames/image: 0-80
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Processing
EM software
ID
Name
Category
2
SerialEM
imageacquisition
4
CTFFIND
CTFcorrection
10
cryoSPARC
initialEulerassignment
11
cisTEM
finalEulerassignment
13
cisTEM
3Dreconstruction
CTF correction
Type: NONE
Particle selection
Num. of particles selected: 193000
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141549 / Algorithm: FOURIER SPACE / Symmetry type: POINT
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