REL PDBe PDBe PDBe 2014-03-06 2014-03-19 2014-06-04 2016-02-17 Cryo-EM structures of the 50S ribosome subunit bound with ObgE Feng B Mandava CS Guo Q Wang J Cao W Li N Zhang Y Zhang Y Wang Z Wu J Sanyal S Lei J Gao N (p)ppGpp, Obg, ribosome assembly, stringent response, GTPase Feng B Mandava CS Guo Q Wang J Cao W Li N Zhang Y Zhang Y Wang Z Wu J Sanyal S Lei J Gao N Structural and functional insights into the mode of action of a universally conserved Obg GTPase. PLOS BIOL. 12 e1001866 e1001866 2014 24844575 doi:10.1371/journal.pbio.1001866 4csu FULLOVERLAP 50S-ObgE complex 50S-ObgE complex 2 1.5 1.5 prokaryotic 50S ribosome subunit false Escherichia coli K-12 K12 cytoplasm 1.5 1.5 ribosome-prokaryote: LSU 50S ObgE Escherichia coli K-12 K12 0.05 0.043 1 monomer true Escherichia coli BL21 BL21 pET28a singleParticle particle 7.5
20mM Tris-HCl, 100mM NH4Cl, 10mM MgCl2
200 mesh copper grid with thin carbon support, glow discharged
 ETHANE 100 FEI VITROBOT MARK IV Blot for 1 seconds before plunging FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 4.0 59000.0 FEI TITAN KRIOS AUTOGRID HOLDER 2011-07-27 FEI EAGLE (4k x 4k) 20 Liquid Nitrogen cooled
Particles were first picked using a method based on a locally normalized cross-correlation function, subjected to correspondence analysis and then manually verified. Then all particles were first classified in two groups, according to the presence or absence of ObgE on the 50S subunit using a modified supervised classification method. The resulting ObgE-containing particles were further applied to another round of 3D classification using RELION. The particles were finally split into four groups in 30 iterations using a final angle sampling of 1.8 degree. One of the four groups was used for final refinement. The refinement was performed using RELION. Amplitude correction using the B-factor sharpening approach was applied to the final volume.
Each particle
 C1 OTHER 5.5 OTHER RELION 102814 emd_2605.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 384.0 384.0 384.0 90.0 90.0 90.0 X Y Z -0.04568339 0.19051541 0.00172401 0.016385 1.5 1.5 1.5 0.045 AUTHOR Reconstruction of 50S-ObgE complex
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 3OFC FLEXIBLE FIT MDFF REAL 1LNZ FLEXIBLE FIT MDFF
The atomic model of the E. coli ObgE was built with MODELLER, using the B. subtilis and T. thermophilus Obg crystal structures (PDB IDs 1LNZ and 1UDX)
REAL