REL PDBe PDBe PDBe 2010-03-09 2010-04-09 2010-12-22 2012-10-24 Cryo-EM structure of S. cerevisiae 10-subunit exosome bound to RNA Malet H Topf M Clare DK Ebert J Bonneau F Basquin J Drazkowska K Tomecki R Dziembowski A Conti E Saibil HR Lorentzen E Exosome, cryo-EM, RNA quality control, exoribonuclease, RNA Malet H Topf M Clare DK Ebert J Bonneau F Basquin J Drazkowska K Tomecki R Dziembowski A Conti E Saibil HR Lorentzen E RNA channelling by the eukaryotic exosome. EMBO REP. 11 936 942 2010 21072061 doi:10.1038/embor.2010.164 S. cerevisiae 10-subunit exosome bound to RNA S. cerevisiae 10-subunit exosome bound to RNA Heterodecamer 11 0.4 0.4 Rrp41 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0276 0.0276 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp42 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0291 0.0291 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp43 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.044 0.044 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp44 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.1137 0.1137 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp45 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0340 0.0340 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp46 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0244 0.0244 1 Monomer true Escherichia coli BL21 (DE3) pET Mtr3 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0273 0.0273 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp4 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0394 0.0394 1 Monomer true Escherichia coli BL21 (DE3) pET Rrp40 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0266 0.0266 1 Monomer true Escherichia coli BL21 (DE3) pET Csl4 Saccharomyces cerevisiae YJM789 Baker's yeast Nucleus, cytoplasm 0.0316 0.0316
Present in sub-stoichiometric amount
1 Monomer true Escherichia coli BL21 (DE3) pET RNA synthetic construct 0.014 0.014
Stem-loop at the 5' end, single stranded RNA at the 3' end
CCCCCGAAAGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA OTHER SINGLE STRANDED true singleParticle particle 0.3 7.5
20 mM Tris-Hcl pH 7.5, 50 mM NaCl, 1 mM DTT
C-flat grid CF-2/2-4C-100
 ETHANE 100 HOMEMADE PLUNGER
Vitrification instrument: Manual plunger
Blot for 2 seconds before plunging FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.3 1.5 3.5 121000.0 121000.0 GATAN HELIUM 100 Objective lens astigmatism was corrected at 150,000 times magnification 0 GENERIC GATAN (4k x 4k) 15 350 25 16. Gatan helium 0 0
Phase flipping
 C1 OTHER 12.0 FSC 0.5 CUT-OFF IMAGIC-5, SPIDER 23000 emd_1709.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 332.8 332.8 332.8 90 90 90 X Y Z -0.573555 9.999890000000001 0.0198479 0.263474 2.6 2.6 2.6 0.03 AUTHOR Cryo-EM map of S. cerevisiae 10-subunit exosome bound to RNA
::::EMDATABANK.org::::EMD-1709::::
 2NN6 C D E F H FLEXIBLE FIT Flex-EM
PDBEntryID_givenInChain. Protocol: Flexible fitting of rigid body. Homology models of yeast subunits have been calculated using MODELLER from the chains C, D, E, F and H of the PDB entry 2NN6. Resulting homology models have been used for flexible fitting into the cryo-EM map.
Cross-correlation, energy REAL 2WP8 A B J FLEXIBLE FIT Flex-EM
PDBEntryID_givenInChain. Protocol: Flexible fitting of rigid body
Cross-correlation, energy REAL 2JA9 A FLEXIBLE FIT Flex-EM
PDBEntryID_givenInChain. Protocol: Flexible fitting of rigid body
Cross-correlation, energy REAL