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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30211 | ||||||||||||||||||
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Title | State 4 of Pre50SH ribosome from RrmJ knock out strain | ||||||||||||||||||
![]() | State 4 | ||||||||||||||||||
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Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.1 Å | ||||||||||||||||||
![]() | Wang W / Li WQ / Ge XL / Yan KG / Mandava CS / Sanyal S / Gao N | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 113.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
Images | ![]() | 51.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 79.3 KB | Display | ![]() |
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Full document | ![]() | 78.4 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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: ![]() ![]() |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 75000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |