REL RCSB RCSB RCSB 2012-02-06 2012-02-10 2013-04-03 2013-04-10 An RNA Degradation Machine Sculpted by Ro Autoantigen and Noncoding RNA Chen X Taylor DW Wang HW Wolin SL exonuclease, Y RNA, degradation machine Chen X Taylor DW Fowler CC Galan JE Wang HW Wolin SL An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA. CELL(CAMBRIDGE,MASS.) 153 166 177 2013 23540697 doi:10.1016/j.cell.2013.02.037 Rsr/Y RNA/PNPase complex Rsr/Y RNA/PNPase complex
The sample was monodisperse and homogeneous.
one Rsr-Y RNA complex binds to one PNPase trimer 3 0.375 0.365 glycerol gradient Ro sixty-related Deinococcus radiodurans 0.062
His-tag Rsr
1 monomer true Escherichia coli RSFDuet-1 Y RNA Deinococcus radiodurans 0.042
Y RNA generated with correct 3' end using hammerhead ribozyme
OTHER OTHER false polynucleotide phosphorylase Deinococcus radiodurans 0.262
Strep-tag PNPase
3 Trimer true Escherichia coli RSFDuet-1 singleParticle particle 0.1 7.5
20 mM HEPES, 50 mM NaCl, 2 mM beta-mercaptoethanol, 1 mM MgCl2, 1 mM MnCl2, 1 mM Petabloc
 NEGATIVE
Grids with adsorbed protein were stained consecutively with 3 droplets of 2% w/v uranyl acetate for 10 seconds each.
Homemade holey carbon grids with a thin layer of carbon over the holes
 NONE OTHER FEI TECNAI 12 FLOOD BEAM BRIGHT FIELD LAB6 120 2.3 0.8 1.2 49000.0 OTHER object lens astigmatism was corrected at 42,000 magnification 2009-07-12 TVIPS TEMCAM-F416 (4k x 4k) 40 20
The particles were selected manually using boxer in EMAN.
Each particle in IMAGIC
 OTHER 25.0 FSC 0.5 CUT-OFF LEGINON, EMAN2, SPARX 9000 50 emd_5389.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 72 72 72 0 0 0 72 72 72 313.92 313.92 313.92 90.0 90.0 90.0 X Y Z -3.97276688 14.19131088 0.0 0.99999869 4.36 4.36 4.36 3.67 AUTHOR negative stain single particle reconstruction of GraFix-prepared Rsr/Y RNA/PNPase complex
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 1E3P A RIGID BODY FIT Chimera
Protocol: Rigid body using Fit-in-Map. A trimer of the crystal structure of PNPase was created using COOT and used for fitting.
Cross-correlation coefficient REAL 1YVP B E F H RIGID BODY FIT Chimera
Protocol: Rigid body using Fit-in-Map. Combined with the double-stranded portion of the misfolded substrate RNA from PDB 2I91.
Cross-correlation coefficient REAL 2I91 C D RIGID BODY FIT Chimera
Protocol: Rigid body using Fit-in-Map. The double-stranded portion of the misfolded substrate RNA from this structure was combined with PDB 1YVP to create a model of Rsr bound by Y RNA and a full substrate RNA with single-stranded tail.
Cross-correlation coefficient REAL