2020-12-23 REL PDBj PDBj PDBj 2019-07-06 2020-07-01 2020-07-01 2020-12-23 National Institutes of Health/National Human Genome Research Institute R35 GM131860 United States Ministry of Education (Korea) NRF-2017M3A9F6029755 Korea, Republic Of Ministry of Education (Korea) 2015R1D1A1A01059097 Korea, Republic Of Ministry of Education (Korea) NRF-2019M3E5D6063903 Korea, Republic Of Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA, focused refinement on RNAP stalk and clamp domains and TFE Hyun J Jun S-H Cho H-S Murakami KS Hyun J Jun S-H Cho H-S Murakami KS Thermococcus kodakraensis RNA polymerase in apo form To Be Published 0353 EMD-9962 other EM volume
EMD-9962 is the same complex refined without local mask
 EMD-9970 associated EM volume EMD-9960 other EM volume EMD-9961 other EM volume EMD-9969 other EM volume 6kf9 FULLOVERLAP Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA 0
RNA polymerase from euryarchaea (Thermococcus kodakarensis) composed of 11 subunits (Rpo1', Rpo1", Rpo2, Rpo3, Rpo4, Rpo5, Rpo6, Rpo7, Rpo10, Rpo11, Rpo12), and in complex with transcription factor E and promoter DNA
Thermococcus kodakarensis KOD1 0.41 singleParticle particle 0.3 8.0 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GRAPHENE OXIDE HOLEY ETHANE 90 278 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 0.002 1.5 3.5 47000.0 100000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Image Cs corrector FEI FALCON II (4k x 4k) INTEGRATING 1-30 3754 1.8 63.0 1
Movie frame data was subjected to motion correction to generate summed micrographs using MotionCor2.
1388666
Approximately 10,000 particles were selected manually. 2D class averages from the manual-picked particles were used as a template for automated particle picking in Relion 2.1.
 Gctf 1.06
Defocus parameters were calculated from motion-corrected micrographs, using Gctf 1.06. Using the defocus parameters, Cs (0.003, after Cs image corrector tuning) and amplitude contrast (0.1), CTF phase flipping and amplitude correction was performed during the reconstruction using Relion 2.1.
 4QIW
PDB file was converted to EM map using e2pdb2mrc.py routine in EMAN2 software package. The reference map was lowpass filtered to 60 angstroms as a startup model.
 1 C1 BACK PROJECTION 3.85 FSC 0.143 CUT-OFF RELION 2.1
Focused refinement on RNAP stalk and clamp domains and TFE was performed by continuing the last iteration of the 3D refinement run of the entire structure (EMD-9962), with the applied local mask
312092 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 4 61916.0 RELION 2.1 emd_9970.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 246.4 246.4 246.4 90.0 90.0 90.0 X Y Z -0.80310476 0.96616983 0.0019456361 0.020877698 1.4 1.4 1.4 0.07 AUTHOR Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko) in complex with transcription factor E (TFE) and DNA, focused refinement emd_9970_msk_1.map emd_9970_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 246.4 246.4 246.4 90.0 90.0 90.0 X Y Z -0.018906686 0.10315703 0.00015193732 0.009819505 1.4 1.4 1.4 AUTHOR Tko RNAP-TFE-DNA (focused refinement) half map 2 emd_9970_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 246.4 246.4 246.4 90.0 90.0 90.0 X Y Z -0.020174714 0.10314409 0.00014898575 0.009792087 1.4 1.4 1.4 AUTHOR Tko RNAP-TFE-DNA (focused refinement) half map 1