2020-01-29 REL RCSB RCSB RCSB 2017-07-10 2017-07-26 2017-10-04 2020-01-29 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM63072 United States TFIIH reconstruction from particles sorted for the XPD FeS-cluster domain using signal-subtracted classification. Greber BJ Nguyen THD Fang J Afonine PV Adams PD Nogales E Greber BJ Nguyen THD Fang J Afonine PV Adams PD Nogales E The cryo-electron microscopy structure of human transcription factor IIH. Nature UK 549 414 417 2017 28902838 doi:10.1038/nature23903 1476-4687 0006 NATUAS EMD-8817 associated EM volume EMD-8816 other EM volume EMD-3802 other EM volume Transcription factor IIH (TFIIH) Transcription factor IIH (TFIIH) 0 Homo sapiens HeLa Nucleus Nucleus 0.49 singleParticle particle 0.0049 7.8 20.0 HEPES-KOH 150.0 KCl potassium chloride 5.0 MgCl2 magnesium chloride 0.5 DTT 2.0 trehalose 1.5 glycerol 0.015 NP-40 substitute Protochips C-flat 4/2 COPPER 400 CARBON HOLEY CARBON CONTINUOUS PLASMA CLEANING AIR ETHANE 100 278.15 FEI VITROBOT MARK IV
3-4 minute incubation, 2 second blot.
Natively purified complex at approx. 10 nM concentration
 FEI TITAN FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 2.0 4.5 37879.0 GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3840 3710 5.0 1-30 4 8300 8.7 40.0
8300 micrographs collected in four session with identical acquisition settings. Sessions lasted 4, 2, 4, and 4 days and yielded 1200, 1700, 2800, and 2600 micrographs.
 1
Micrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected.
1500000
Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking.
 CTFFIND 4 run from within RELION
Correction within RELION based on values determined in CTFFIND4.
 EMD-8131
Box and pixel size were adjusted before initial refinement.
 2 FOURIER SPACE 4.4 FSC 0.143 CUT-OFF RELION 1.4
RELION 3D auto-refinement (gold standard). The final 3D classification used signal-subtracted particle images. The final reconstruction used the corresponding un-subtracted particle images.
88700 PROJECTION MATCHING RELION 1.4
Maximum-likelihood 3D classification within RELION.
 PROJECTION MATCHING RELION 1.4
Maximum-likelihood 3D refinement within RELION.
 6 RELION 1.4
Signal-subtracted classification in RELION 1.4, using 6 classes.
 emd_8817.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 337.92 337.92 337.92 90.0 90.0 90.0 X Y Z -0.06940234 0.1495091 -0.0000080399 0.00466946 1.32 1.32 1.32 0.027 AUTHOR TFIIH reconstruction from particles sorted for the FeS-cluster domain using signal-subtracted classification. RIGID BODY FIT
Fitting of a refined coordinate model obtained from a 4.4 Angstrom reconstruction of TFIIH from the same initial dataset (PDB ID 5OF4).
REAL