REL PDBe PDBe PDBe 2006-07-17 2006-07-18 2006-07-18 2011-05-26 Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation. Passmore LA Booth CR Venien-Bryan C Ludtke SJ Fioretto C Johnson LN Chiu W Barford D Passmore LA Booth CR Venien-Bryan C Ludtke SJ Fioretto C Johnson LN Chiu W Barford D Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation. MOLECULAR CELL 20 855 866 2005 16364911 doi:10.1016/j.molcel.2005.11.003 Anaphase-Promoting Complex Anaphase-Promoting Complex
The APC was freshly purified before grid preparation.
monomer 1 1.7 1.7 Anaphase-Promoting Complex, Cyclosome Saccharomyces cerevisiae CDC16-TAP BJ2168 budding yeast 1.7 1.7
Endogenous APC was purified using a TAP tag present at the C-terminus of the Cdc16 subunit. The APC has 13 different protein subunits. There are multiple copies of specific APC subunits, consistent with a total mass of 1.7 MDa.
Monomer true Saccharomyces cerevisiae GO:0005680 singleParticle particle 0.125 8.0
20 mM HEPES, 150 mM NaCl, 2 mM EGTA, 3 mM DTT, 1 mM Magnesium acetate, 0.015% (w/v) n-Dodecyl B-D-maltoside (DDM)
Quantifoil R2/2, 200 mesh with an additional layer of freshly floated carbon
 ETHANE 80 OTHER
Vitrification instrument: Vitrobot
4 ul sample was applied to the grid then blotted two times one second on both sides before plunging into liquid ethane. JEOL 2010F FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1 1.8 3.5 50000.0 69200.0 GATAN LIQUID NITROGEN 92 GATAN ULTRASCAN 4000 (4k x 4k) 15 650 15 16. Side entry liquid-nitrogen cooled cryo specimen holder
Complete phase flipping and amplitude weighting with wiener filtration using the 1D structure factor
 C1 OTHER 20.0 FSC 0.5 CUT-OFF eman
Due to sample heterogeneity, the data could be separated into two main groups using a multirefinement procedure. Structure A (7500 particles) is in EMD-1174. This is structure B (6800 particles).
19384 emd_1245.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 144 144 144 -72 -72 -72 144 144 144 312.192 312.192 312.192 90 90 90 X Y Z -0.718464 7.37117 -0.00000000240875 1.0 2.168 2.168 2.168 2.45 Structure of Saccharomyces cerevisiae Anaphase-Promoting Complex/Cyclosome (APC). Due to heterogeneity, we obtained 2 structures (A and B) from our dataset. This is "structure B" while EMD-1174 is "structure A".
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 RIGID BODY FIT Foldhunter, DockEM
Protocol: rigid body. 15 or 18 consecutive TPR motifs modelled from PP5 (1A17) were docked as rigid structures into the APC density map using Foldhunter or DockEM. Both programs produced similar results.
Cross-correlation