RELPDBePDBePDBe2016-03-292016-04-062016-04-062016-04-13Electron cryo-microscopy of CSN-SCF-N8 complexMosadeghi RReichermeier KMWinkler MSchreiber AReitsma JMZhang YStengel FCao JKim MSweredoski MJHess SLeitner AAebersold RPeter MDeshaies RJEnchev RICOP9 signalosome, Cullin-RING ligase, SCF, deneddylationMosadeghi RReichermeier KMWinkler MSchreiber AReitsma JMZhang YStengel FCao JKim MSweredoski MJHess SLeitner AAebersold RPeter MDeshaies RJEnchev RIStructural and kinetic analysis of CSN activation and the cullin-RING ubiquitin ligase deneddylation cycleElife5201627031283doi:10.7554/eLife.12102CSN5H138A-N8_SCF/Skp2CSN5H138A-N8_SCF/Skp2one CSN monomer and one SCF monomer140.5Csn1Homo sapiensHuman0.0551monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ13098Csn2Homo sapiensHuman0.0511monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemP61201Csn3Homo sapiensHuman0.0471monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ9UNS2Csn4Homo sapiensHuman0.0461monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ9BT78Csn5Homo sapiensHuman0.037His6 tag on the N-terminus1monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ92905Csn6Homo sapiensHuman0.0361monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ7L5N1Csn7bHomo sapiensHuman0.02961monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ9H9Q2Csn8Homo sapiensHuman0.0231monomer (part of the CSN)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ99627Cul1Homo sapiensHuman0.089StrepII2x tag on the N-terminus1monomer (part of SCF)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemQ13616Rbx1Homo sapiensHuman0.0121monomer (part of SCF)trueHigh Five insect cellsTrichoplusia niBTI-TN-5B1-4multibac systemP62877Nedd8Homo sapiensHuman0.0091monomer (part of SCF)trueEscherichia coliBL21see publicationQ15843Skp1Homo sapiensHumansee Enchev et al 2012 Cell Reports for details of the used construct1monomer (part of SCF)trueEscherichia coliBL21see publicationP63208Skp2Homo sapiensHumansee Enchev et al 2012 Cell Reports for details of the used construct1monomer (part of SCF)trueEscherichia coliBL21see publicationQ13309Cks1Homo sapiensHuman0.0096see Enchev et al 2012 Cell Reports for details of the used construct1monomer (part of SCF)trueEscherichia coliBL21see publicationP61024singleParticleparticle0.17.615 mM HEPES, pH 7.6, 100 mM NaCl, 0.5 mM DTTQuantifoil grids (R1.2/1.3 Cu 400 mesh), freshly coated with an extra layer of thin carbon and glow-discharged for 2 min at 50 mA and 0.2 mbar vacuumETHANE100120HOMEMADE PLUNGERthe sample was diluted to 0.1 mg/ml and 2 ul were applied to Quantifoil grids (R1.2/1.3 Cu 400 mesh), freshly coated with an extra layer of thin carbon and glow-discharged for 2 min at 50 mA and 0.2 mbar vacuum. The grids were manually blotted to produce a thin sample film and plunge-frozen into liquid ethaneFEI TITAN KRIOSFLOOD BEAMBRIGHT FIELDFIELD EMISSION GUN3002.72.55.060000.080460.0FEI TITAN KRIOS AUTOGRID HOLDER90110100Objective lens astigmatism was corrected manually at a nominal magnification of 100,000x2015-05-12FEI FALCON II (4k x 4k)25Microgrpahs were the average of six frames recorded by the direct electron detector. All micrographs were initially visually inspected and only those with appropriate ice thickness as well as Thon rings in their power spectra showing regularity and extending to 6 A or beyond were used for subsequent analysis.CTF-estimation and subsequent correction were performed using RELION (Scheres, 2012) and CTFFIND3 (Mindell and Grigorieff, 2003). All micrographs were initially visually inspected and only those with appropriate ice thickness as well as Thon rings in their power spectra showing regularity and extending to 6 A or beyond were used for subsequent analysis. In order to generate 2D references for automated particle selection, ~ 4,000 single particles were manually picked and subjected to 2D classification in RELION. Six well-defined 2D class averages were selected, low-pass filtered to 35 A to prevent reference bias, and used as references. Approximately 150,000 single particles were automatically selected and subjected to reference-free 2D and 3D classification, in order to de-select the particles, which resulted in poorly defined or noisy averages. Approximately half of these single particles resulted in a well-defined 3D class average, which resembled the previously published negative stain EM map of the same complex (Enchev et al., 2012). This dataset was subject to 3D auto-refinement in RELION, using a version low-pass filtered to 50 A as an initial reference. The converged map was further post-processed in RELION, using MTF-correction, FSC-weighting and a soft spherical mask with a 5-pixel fall-off.micrographsC17.2OTHERrelion, CTFFIND3750001LDKABCDERIGID BODY FITChmierasome domains were fitted separately to account for conformational rearrangements, see publication for detailsoverlapREAL4D10ABCDEFHRIGID BODY FITChmieraCsn7b was modeled using Csn7a as a template on the Phyre2 server; some domains were fitted separately to account for conformational rearrangements, see publication for detailsoverlapREAL1FQVABRIGID BODY FITChmieraoverlapREAL