CryoEM reconstruction of human IKK1, intermediate conformation 2

2026-02-25 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION em_software pdbx_audit_support _em_software.name _pdbx_audit_support.funding_organization EXPERIMENTAL_PREPARATION em_sample_support _em_sample_support.grid_type AUTHOR_SUPPORTING_EVIDENCE pdbx_audit_support _pdbx_audit_support.funding_organization DATABASE_REFERENCES chem_comp_atom chem_comp_bond database_2 _database_2.pdbx_DOI _database_2.pdbx_database_accession STRUCTURE_SUMMARY audit_author em_admin pdbx_entry_details _audit_author.name _em_admin.last_update RCSB RCSB 2016-10-24 2016-11-09 2016-11-09 2026-02-25 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 Cancer Institute (NIH/NCI) CA141722 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM071862 United States CryoEM reconstruction of human IKK1, intermediate conformation 2 Lyumkis D Ghosh G kinase, conserved helix-loop-helix, transcription, oncogene, TRANSFERASE 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-8436 other EM volume EMD-8438 other EM volume EMD-8439 other EM volume 5tqx FULLOVERLAP EMDB EMD-8437 associated EM volume EMDB EMD-8436 other EM volume EMDB EMD-8438 other EM volume EMDB EMD-8439 other EM volume PDB 5TQW unspecified PDB 5TQY unspecified Inhibitor of KappaB Kinase 1 dimer Inhibitor of KappaB Kinase 1 dimer 0 1

dimer

Homo sapiens 0.15 Inhibitor of nuclear factor kappa-B kinase subunit alpha Homo sapiens 0.075146945 2 Spodoptera frugiperda LEVO DPEFGAGGPWEMRERLGTGGFGNVCLYQHRELDLKIAIKSCRLELSTKNRERWCHEIQIMKKLNHANVVKACDVPEELNI LIHDVPLLAMEYCSGGDLRKLLNKPENCCGLKESQILSLLSDIGSGIRYLHENKIIHRDLKPENIVLQDVGGKIIHKIID LGYAKDVDQGELCTEFVGTLQYLAPELFENKPYTATVDYWSFGTMVFECIAGYRPFLHHLQPFTWHEKIKKKDPKCIFAC EEMSGEVRFSSHLPQPNSLCSLIVEPMENWLQLMLNWDPQQRGGPVDLTLKQPRCFVLMDHILNLKIVHILNMTSAKIIS FLLPPDESLHSLQSRIERETGINTGSQELLSETGISLDPRKPASQCVLDGVRGCDSYMVYLFDKSKTVYEGPFASRSLSD CVNYIVQDSKIQLPIIQLRKVWAEAVHYVSGLKEDYSRLFQGQRAAMLSLLRYNANLTKMKNTLISASQQLKAKLEFFHK SIQLDLERYSEQMTYGISSEKMLKAWKEMEEKAIHYAEVGVIGYLEDQIMSLHAEIMELQKSPYGRRQGDLMESLEQRAI DLYKQLKHRPSDHSYSDSTEMVKIIVHTVQSQDRVLKELFGHLSKLLGCKQKIIDLLPKVEVALSNIKEADNTVMFMQGK RQKEIWHLLKIACTQ O15111 2.7.11.10 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 6 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 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

PHASE FLIPPING AND AMPLITUDE CORRECTION

common lines model generated using OptiMod and EMAN1

C2 FOURIER SPACE 5.4 FSC 0.143 CUT-OFF FREALIGN 9.11 30540 PROJECTION MATCHING RELION 1.3 PROJECTION MATCHING FREALIGN 9.11 3 FREALIGN 9.11

Three conformational states were captured using a four-model classification, with the last class corresponding to particles that produced a low-resolution reconstruction (increasing this number to 5 or 6 classes did not increase the number of recovered conformational states). Although three conformational states were recovered during classification, it is likely these states are not discrete, and a continuum of movement about the central hinge exists, which is indicated by the relatively homogeneous distribution of particles within the classes.

emd_8437.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 251.51999 251.51999 251.51999 90.0 90.0 90.0 X Y Z -0.085789174 0.17421143 0.0004400544 0.008512164 1.31 1.31 1.31 0.045 AUTHOR ::::EMDATABANK.org::::EMD-8437:::: CryoEM reconstruction of human IKK1, intermediate conformation 2, final map FLEXIBLE FIT FSC 0.5 REAL 340.0 emd_8437_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 251.51999 251.51999 251.51999 90.0 90.0 90.0 X Y Z -0.18306398 0.2589646 0.0008745095 0.018579938 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::EMD-8437:::: CryoEM reconstruction of human IKK1, intermediate conformation 2, unmasked half map 1 emd_8437_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 251.51999 251.51999 251.51999 90.0 90.0 90.0 X Y Z -0.17530783 0.27888727 0.000864763 0.018678656 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::EMD-8437:::: CryoEM reconstruction of human IKK1, intermediate conformation 2, unmasked half map 2