2026-09-30 REL RCSB RCSB RCSB 2025-01-13 2025-02-19 2025-02-19 2026-09-30 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM131860 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM047477 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM098399 United States Structure of a native Drosophila melanogaster Pol II Elongation Complex Venette-Smith NL Vishwakarma RK Dollinger R Schultz J Venkatakrishnan V Babitzke P Anand G Gilmour DS Armache J-P Murakami K polymerase, Pol II, transcription, mRNA Venette-Smith NL Vishwakarma RK Venkatakrishnan V Dollinger R Schultz J Babitzke P Anand G Gilmour DS Armache JP Murakami KS Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster. Nat Commun UK 17 2026 42711332 doi:10.1038/s41467-026-75963-0 2041-1723 EMDB EMD-48624 associated EM volume Natively purified Pol II elongation complex from Drosophila melanogaster. This entry contains a Coulomb potential density map which is a mix of polymerases with and without stalk. Natively purified Pol II elongation complex from Drosophila melanogaster. This entry contains a Coulomb potential density map which is a mix of polymerases with and without stalk. 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
This entry represents a native Pol II elongation complex which is the best-resolved overall reconstruction from this dataset. It is composed of particles with Rpb4/Rpb7 stalk, as well as without Rpb4/Rpb7 stalk
Drosophila melanogaster 930 singleParticle particle 1.0 7.5 150.0 NaCl Sodium chloride 10.0 HEPES-HCl HEPES 5.0 Glycerol Glycerol 1.0 EDTA EDTA 350.0 FLAG FLAG peptide
10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
 Quantifoil GOLD 200 GOLD HOLEY GLOW DISCHARGE ETHANE 100 4 FEI VITROBOT MARK IV
double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes
 TFS TALOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 2.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 4 31103 50.65
Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360
 1 2349308
Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (2,349,308) is the starting number of particles after initial cleanup and 3D classification of the data.
 cryoSPARC 4.3.1
'Patch CTF Estimation' in cryoSPARC
PHASE FLIPPING AND AMPLITUDE CORRECTION 'Ab initio' function in cryoSPARC 1 C1 BACK PROJECTION 2.86 FSC 0.143 CUT-OFF cryoSPARC 4.3.1
The data was processed using cryoSPARC to 2.96 A from 876,764 particles. It was later post-processed using CryoSieve to select the final number of particles, yielding 2.86 A.
68716 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1
'Non-Uniform Refinement' in cryoSPARC
 emd_48624.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.0 2.7697618 0.011336053 0.061930116 1.1538 1.1538 1.1538 0.4 AUTHOR Refined, unsharpened Coulomb potential density map. Particles extracted in 440x440 Fourier cropped to 360x360. 50.0 emd_48624_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -1.4596702 5.106633 0.011336052 0.09338829 1.1538 1.1538 1.1538 AUTHOR Refined, auto-sharpened Coulomb potential density map with Bfactor = -47.8 emd_48624_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -1.2659607 2.96373 0.0015895921 0.13113528 1.1538 1.1538 1.1538 AUTHOR Half-map 1 emd_48624_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -1.3156027 3.124386 0.0016140905 0.13132642 1.1538 1.1538 1.1538 AUTHOR Half-map 2