REL PDBj RCSB PDBj 2013-04-27 2013-06-12 2013-06-12 2013-08-28 Cryo-EM structures of the late-stage assembly intermediates of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain. Li N Chen Y Guo Q Zhang Y Yuan Y Ma C Deng H Lei J Gao N Ribosome biogenesis, ribosome assembly intermediate, RNA folding Li N Chen Y Guo Q Zhang Y Yuan Y Ma C Deng H Lei J Gao N Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. NUCLEIC ACIDS RES. 41 7073 7083 2013 23700310 doi:10.1093/nar/gkt423 3j3w FULLOVERLAP Assembly intermediate of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain Assembly intermediate of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain 1 assembly intermediate of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain false Bacillus subtilis Bacillus subtilis subsp. subtilis str. 168 ribosome-prokaryote: LSU 50S singleParticle particle 7.5
100mM NH4Cl, 20mM Tris-HCl, 10mM MgOAc2, 1mM TCEP
 ETHANE 100 FEI VITROBOT MARK IV Blot for 20 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 2011-12-06 FEI EAGLE (4k x 4k) 20
This is one of the classified groups with the software RELION
Each particle
 OTHER 10.7 OTHER RELION 27652 emd_5643.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 -127 -127 -127 256 256 256 384.0 384.0 384.0 90.0 90.0 90.0 X Y Z -3.26229954 10.90894222 0.0 1.0 1.5 1.5 1.5 2.0 AUTHOR 3D classification of the assembly intermediates of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain
::::EMDATABANK.org::::EMD-5643::::
 2AW4 FLEXIBLE FIT S2S, modeRNA, MODELLER, MDFF
Atom models of the 23S and 5S rRNAs were built using the software S2S and modeRNA, with the crystal structures of the 50S subunits from E. coli (PDB ID: 2AW4) and Thermus thermophilus (PDB ID: 2J01) as template. Models of ribosomal proteins, L1, L3, L4, L6, L10, L13, L14, L15, L17, L19, L20, L21, L22, L23, L24, L27, L29, L30, L31, L32, L33, L34, L35 and L36 were downloaded from the SWISS-MODEL Repository. The others, including L2, L5, L11, L16, L18 and L28 were modeled using MODELLER with crystal structures of E. coli and T. thermophilus 50S subunits as templates.The combined atomic model of the B. subtilis 50S subunit was docked into a high resolution mature 50S density map and optimized using MDFF. This optimized model was docked into the EM density using Chimera and flexible fitted into the density using MDFF
Cross-correlation coefficient REAL 2J01 S2S, modeRNA, MODELLER, MDFF
Atom models of the 23S and 5S rRNAs were built using the software S2S and modeRNA, with the crystal structures of the 50S subunits from E. coli (PDB ID: 2AW4) and Thermus thermophilus (PDB ID: 2J01) as template. Models of ribosomal proteins, L1, L3, L4, L6, L10, L13, L14, L15, L17, L19, L20, L21, L22, L23, L24, L27, L29, L30, L31, L32, L33, L34, L35 and L36 were downloaded from the SWISS-MODEL Repository. The others, including L2, L5, L11, L16, L18 and L28 were modeled using MODELLER with crystal structures of E. coli and T. thermophilus 50S subunits as templates.The combined atomic model of the B. subtilis 50S subunit was docked into a high resolution mature 50S density map and optimized using MDFF. This optimized model was docked into the EM density using Chimera and flexible fitted into the density using MDFF
Cross-correlation coefficient REAL