+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23539 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cfr-modified 50S subunit from Escherichia coli | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Cfr-modified 50S subunit / RIBOSOME | |||||||||
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 / regulation of cell growth / ribosomal large subunit assembly / 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 / regulation of cell growth / ribosomal large subunit assembly / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Stojkovic V / Myasnikov AG | |||||||||
Funding support | United States, 1 items
| |||||||||
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 AG / Young ID / Palla A / Venkataramanan S / Floor S / Fraser JS / Frost A / Tawfik DS / Fujimori DG | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23539.map.gz | 19.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23539-v30.xml emd-23539.xml | 45 KB 45 KB | Display Display | EMDB header |
Images | emd_23539.png | 141.4 KB | ||
Filedesc metadata | emd-23539.cif.gz | 10.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23539 | HTTPS FTP |
-Validation report
Summary document | emd_23539_validation.pdf.gz | 409.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23539_full_validation.pdf.gz | 409.4 KB | Display | |
Data in XML | emd_23539_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_23539_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23539 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23539 | HTTPS FTP |
-Related structure data
Related structure data | 7lvkMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23539.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Escherichia coli 50S subunit
+Supramolecule #1: Escherichia coli 50S subunit
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L9
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: MAGNESIUM ION
+Macromolecule #32: SODIUM ION
+Macromolecule #33: ZINC ION
+Macromolecule #34: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.5 / Component - Concentration: 10.0 mM / Component - Formula: TRIS / Component - Name: TRIS / Details: Buffer A |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV Details: Blot Force 5 Blot Time 10sec Hum 95% Temperature 10C Waiting time 1 min. |
Details | 50S ribosomal subunit was purified from E. coli MRE600 using modified version of previously published protocol (Mehta et al. 2012) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 86.0 K / Max: 130.0 K |
Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 0-80 / Number grids imaged: 1 / Number real images: 2055 / Average exposure time: 8.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | PDB-7lvk: |