+Open data
-Basic information
Entry | Database: PDB / ID: 7lvk | |||||||||
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Title | Cfr-modified 50S subunit from Escherichia coli | |||||||||
Components |
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Keywords | RIBOSOME / Cfr-modified 50S subunit | |||||||||
Function / homology | Function and homology information positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / regulation of cell growth / large ribosomal subunit / ribosome binding / transferase activity ...positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / regulation of cell growth / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Stojkovic, V. / Myasnikov, A.G. / Frost, A. / Fujimori, D.G. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Investigating antibiotic resistance of a ribosomal-RNA methylating enzyme through directed evolution Authors: Tsai, K. / Stojkovic, V. / Noda-Garcia, L. / Myasnikov, A.G. / Young, I.D. / Palla, A. / Venkataramanan, S. / Floor, S. / Fraser, J.S. / Frost, A. / Tawfik, D.S. / Fujimori, D.G. | |||||||||
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 | 7lvk.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7lvk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7lvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lvk_validation.pdf.gz | 989.4 KB | Display | wwPDB validaton report |
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Full document | 7lvk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7lvk_validation.xml.gz | 131 KB | Display | |
Data in CIF | 7lvk_validation.cif.gz | 241 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/7lvk ftp://data.pdbj.org/pub/pdb/validation_reports/lv/7lvk | HTTPS FTP |
-Related structure data
Related structure data | 23539MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules IJ
#1: RNA chain | Mass: 941823.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1273279017 |
+50S ribosomal protein ... , 28 types, 28 molecules KLMNOPRSTUVWXYZabcdefghijklm
-Non-polymers , 4 types, 2897 molecules
#31: Chemical | ChemComp-MG / #32: Chemical | ChemComp-NA / | #33: Chemical | ChemComp-ZN / | #34: Water | ChemComp-HOH / | |
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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: Escherichia coli 50S subunit / Type: RIBOSOME / Entity ID: #1-#30 / Source: NATURAL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: Buffer A |
Buffer component | Conc.: 10 mM / Name: TRIS / Formula: TRIS |
Specimen | 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) |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K Details: Blot Force 5 Blot Time 10sec Hum 95% Temperature 10C Waiting time 1 min |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 300 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | 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: 2055 |
Image scans | Sampling size: 5 µm / Width: 7676 / Height: 7420 / Movie frames/image: 80 / Used frames/image: 0-80 |
-Processing
EM software |
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CTF correction | Details: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 162713 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141549 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |