2020-01-29 REL RCSB RCSB RCSB 2016-10-24 2016-11-09 2016-11-09 2020-01-29 National Institutes of Health/Office of the Director DP5 OD021396-01 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI064326 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM071862 United States National Institutes of Health/National Cancer Institute (NIH/NCI) CA141722 United States CryoEM reconstruction of hIKK1 in the most open state, conformation 1 Lyumkis D Ghosh G Polley S Biswath T Huang D Passos DO Polley S Passos DO Huang DB Mulero MC Mazumder A Biswas T Verma IM Lyumkis D Ghosh G Structural Basis for the Activation of IKK1/ alpha. Cell Rep US 17 1907 1914 2016 27851956 doi:10.1016/j.celrep.2016.10.067 2211-1247 EMD-8439 associated EM volume EMD-8436 other EM volume EMD-8437 other EM volume EMD-8438 other EM volume Inhibitor of KappaB Kinase 1 hexamer Inhibitor of KappaB Kinase 1 hexamer 0 1
hexamer
Homo sapiens Spodoptera frugiperda SF9 pFastBacHTa 0.45 Inhibitor of Kappa B Kinase 1 Homo sapiens Spodoptera frugiperda LEVO DPEFGAGGPWEMRERLGTGGFGNVCLYQHRELDLKIAIKSCRLELSTKNR ERWCHEIQIMKKLNHANVVKACDVPEELNILIHDVPLLAMEYCSGGDLRK LLNKPENCCGLKESQILSLLSDIGSGIRYLHENKIIHRDLKPENIVLQDV GGKIIHKIIDLGYAKDVDQGELCTEFVGTLQYLAPELFENKPYTATVDYW SFGTMVFECIAGYRPFLHHLQPFTWHEKIKKKDPKCIFACEEMSGEVRFS SHLPQPNSLCSLIVEPMENWLQLMLNWDPQQRGGPVDLTLKQPRCFVLMD HILNLKIVHILNMTSAKIISFLLPPDESLHSLQSRIERETGINTGSQELL SETGISLDPRKPASQCVLDGVRGCDSYMVYLFDKSKTVYEGPFASRSLSD CVNYIVQDSKIQLPIIQLRKVWAEAVHYVSGLKEDYSRLFQGQRAAMLSL LRYNANLTKMKNTLISASQQLKAKLEFFHKSIQLDLERYSEQMTYGISSE KMLKAWKEMEEKAIHYAEVGVIGYLEDQIMSLHAEIMELQKSPYGRRQGD LMESLEQRAIDLYKQLKHRPSDHSYSDSTEMVKIIVHTVQSQDRVLKELF GHLSKLLGCKQKIIDLLPKVEVALSNIKEADNTVMFMQGKRQKEIWHLLK IACTQ singleParticle particle 2.5 7.5 150.0 NaCl sodium chloride 20.0 C4H12ClNO3 Tris-HCl 5.0 C4H10O2S2 DTT 5.0 C3H8O3 Glycerol C-flat-1.2/1.3 COPPER 400 CARBON HOLEY PLASMA CLEANING AIR ETHANE 80 277 HOMEMADE PLUNGER
Sample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grids (Protochips), adsorbed for 30 seconds, and then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.1 5.2 22500.0 38167.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 5.0 1-50 1 2918 10.0 40.0
The dose was fractionated over 50 raw frames collected over a 10 second exposure time (200 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~6.5 e-/pixel/sec. 2918 movies were collected and recorded at a nominal magnification of 22,500, corresponding to a pixel size of 1.31 A at the specimen level. The individual frames were gain-corrected, then aligned and summed using a GPU-enabled whole frame alignment program (Li et al., 2013), and exposure-filtered (Grant and Grigorieff, 2015).
 1 230242 CTFFIND within Appion
within Relion and Frealign
common lines model generated using OptiMod and EMAN1
 D3 FOURIER SPACE 5.9 FSC 0.143 CUT-OFF FREALIGN 9.11 1432 PROJECTION MATCHING RELION 1.3 PROJECTION MATCHING FREALIGN 9.11 FREALIGN 9.11
During 2D alignment and classification, we noticed that a small percentage of particles apparently formed multiple dimers stacked side-by-side. After several rounds of sub-classification, it became apparent that this small percentage of particles actually corresponded to an oligomer of IKK1 dimers. An ab initio initial model was generated from the subset of particles using OptiMod, which showed that the oligomer was clearly hexameric in nature. 3D classifications and refinements were performed in a similar fashion as for the dimers. Only one conformational state was identified (despite asking for the recovery of up to 5 classes), which was refined to ~5.9 A resolution
 emd_8439.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.07212129 0.13111335 -0.00032097686 0.0055240183 1.31 1.31 1.31 0.035 AUTHOR CryoEM reconstruction of human IKK1, hexameric composition, final map 380 emd_8439_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.7158288 0.8005622 -0.0006801326 0.05035735 1.31 1.31 1.31 AUTHOR CryoEM reconstruction of human IKK1, hexameric composition, half map 2, unfiltered and unmasked emd_8439_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.7986551 0.76645327 -0.0006117235 0.049638223 1.31 1.31 1.31 AUTHOR CryoEM reconstruction of human IKK1, hexameric composition, half map 1, unfiltered and unmasked