|Entry||Database: EMDB / ID: 1884|
|Title||RsgA-30S ribosomal subunit-GMPPNP complex|
|Keywords||ribosome biogenesis / RsgA / yjeq / circularly permutated GTPase / 30S subunit|
|Sample||RsgA-30S ribosome-GMPPNP complex|
|Source||Escherichia coli dh5[alpha] / bacteria / image: Escherichia coli|
Escherichia coli / bacteria / /
|Map data||This is the map of RsgA-30S-GMPPNP complex|
|Method||single particle reconstruction, at 9.8 Å resolution|
|Authors||Guo Q / Yuan Y / Xu Y / Feng B / Liu L / Chen K / Lei J / Gao N|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 13100-13105|
Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 13100-13105 Yorodumi Papers
|Validation Report||PDB-ID: 2ykr|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 24, 2011 / Header (metadata) release: Nov 17, 2011 / Map release: Nov 17, 2011 / Last update: Mar 13, 2013|
Downloads & links
|File||emd_1884.map.gz (map file in CCP4 format, 7631 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.9 Å|
CCP4 map header:
-Entire RsgA-30S ribosome-GMPPNP complex
|Entire||Name: RsgA-30S ribosome-GMPPNP complex / Number of components: 3|
Oligomeric State: One RsgA binds to one 30S ribosome in the presence of one GMPPNP
|Mass||Theoretical: 800 kDa / Experimental: 800 kDa / Measured by: Sedimentation|
-Component #1: ribosome-prokaryote, 30S ribosome
|Ribosome-prokaryote||Name: 30S ribosome / a.k.a: 30S ribosome / Prokaryote: SSU 30S / Recombinant expression: No|
|Source||Species: Escherichia coli dh5[alpha] / bacteria / image: Escherichia coli|
-Component #2: protein, RsgA
|Protein||Name: RsgA / a.k.a: RsgA / Oligomeric Details: monomer / Recombinant expression: Yes|
|Source||Species: Escherichia coli / bacteria / / / Strain: DH5a|
|Source (engineered)||Expression System: Escherichia coli bl21 / bacteria / image: Escherichia coli|
|Source (natural)||Organelle: cellular|
-Component #3: ligand, Guanylyl Imidodiphosphate
|Ligand||Name: Guanylyl Imidodiphosphate / a.k.a: GMP-PNP / Recombinant expression: No|
|Sample solution||Buffer solution: 20 mM Tris-HCl,150 mM NH4Cl,10 mM Mg(OAc)2 / pH: 7.6|
|Support film||300 mesh Quantifoil|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 4 K|
Details: Vitrification instrument: FEI Vitrobot. Rapid-freezing in liquid ethane
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 3850 nm|
|Specimen Holder||Holder: Eucentric / Model: OTHER|
|Camera||Detector: FEI EAGLE (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 77483 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Reference based / Software: SPIDER / CTF correction: Maps from each defocus group|
Details: The final map is processed with an additional amplitude correction procedure.
Resolution: 9.8 Å / Resolution method: FSC 0.5
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