+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30211 | ||||||||||||||||||
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Title | State 4 of Pre50SH ribosome from RrmJ knock out strain | ||||||||||||||||||
Map data | State 4 | ||||||||||||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.1 Å | ||||||||||||||||||
Authors | Wang W / Li WQ / Ge XL / Yan KG / Mandava CS / Sanyal S / Gao N | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: To Be Published Title: Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation Authors: Wang W / Li WQ / Ge XL / Yan KG / Mandava CS / Sanyal S / Gao N | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30211.map.gz | 113.9 MB | EMDB map data format | |
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Header (meta data) | emd-30211-v30.xml emd-30211.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_30211.png | 51.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30211 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30211 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30211.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | State 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : State 4 of pre50SH ribosome
Entire | Name: State 4 of pre50SH ribosome |
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Components |
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-Supramolecule #1: State 4 of pre50SH ribosome
Supramolecule | Name: State 4 of pre50SH ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32 Details: State 4 of pre50SH ribosome from RrmJ knock out E.coli strain |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 Details: Solutions were made fresh form concentrated to avoid microbial contamination. |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 7000.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2 seconds before plunging. |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 75000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 3-28 / Number grids imaged: 1 / Number real images: 1262 / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 235600 Details: Images were binned and lowpass filtered for autopicking. |
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CTF correction | Software - Name: CTFFIND (ver. 3.0) Details: CTF amplitude correction was performed following 3D reconstruction. |
Startup model | Type of model: OTHER Details: The model was a low resolution 50S ribosome generated from our own data. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4) / Details: Relion software was used in the reconstruction. |
Final 3D classification | Number classes: 6 / Avg.num./class: 15300 / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4) / Details: Relion software was used in the reconstruction. |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 1372 |
Details | The images were normalized and manually selected. |