2026-09-09 REL RCSB RCSB RCSB 2025-01-13 2025-02-19 2025-02-19 2026-09-09 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 Nucleosome Elongation Complex (Pol II EC-nucleosome). Overall structure 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 2026 doi:10.1038/s41467-026-75963-0 2041-1723 EMD-48823 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of nucleosome
 EMD-4882 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of Pol II
 EMD-48626 other EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
 EMD-48624 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex
 EMD-48623 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
 EMD-48622 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
 EMD-48621 other EM volume
Structure of native Drosophila melanogaster DLST
 EMD-48620 other EM volume
Structure of a native Drosophila melanogaster hexameric nucleosome
 EMD-48619 other EM volume
Structure of a native Drosophila melanogaster octameric nucleosome
 EMDB EMD-48625 associated EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Consensus map
 EMDB EMD-48823 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of nucleosome
 EMDB EMD-4882 focused EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Focused refinement of Pol II
 EMDB EMD-48626 other EM volume
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
 EMDB EMD-48624 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex
 EMDB EMD-48623 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
 EMDB EMD-48622 other EM volume
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
 EMDB EMD-48621 other EM volume
Structure of native Drosophila melanogaster DLST
 EMDB EMD-48620 other EM volume
Structure of a native Drosophila melanogaster hexameric nucleosome
 EMDB EMD-48619 other EM volume
Structure of a native Drosophila melanogaster octameric nucleosome
 PDB 9MU9 unspecified
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
 PDB 9MU8 unspecified
Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
 PDB 9MU7 unspecified
Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
 PDB 9MU6 unspecified
Structure of native Drosophila melanogaster DLST
 PDB 9MU5 unspecified
Structure of a native Drosophila melanogaster hexameric nucleosome
 PDB 9MU4 unspecified
Structure of a native Drosophila melanogaster octameric nucleosome
 Native purified Nucleosome Elongation Complex from Drosophila melanogaster Native purified Nucleosome Elongation Complex from Drosophila melanogaster 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
An overall structure of a native purified Nucleosome Elongation Complex (Pol II EC - nucleosome), where the Pol II and nucleosome are both at a lower resolution due to their motion in respect to each other
Drosophila melanogaster 0.750 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 4197404
Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (4,197,404) is the starting number of particles after initial cleanup and 3D classification of the data representing Pol II and nucleosome subsets, respectively.
 cryoSPARC 4.3.1
'Patch CTF Estimation' in cryoSPARC
PHASE FLIPPING AND AMPLITUDE CORRECTION 'Ab initio' function in cryoSPARC 1 C1 BACK PROJECTION 7.8 FSC 0.143 CUT-OFF cryoSPARC 4.3.1
The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an individual focus on the nucleosome and Pol II
36552 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1
'Non-Uniform Refinement' in cryoSPARC
 emd_48625.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 0.8878653 0.004199319 0.030429076 1.1538 1.1538 1.1538 0.1 AUTHOR Refined, unsharpened Coulomb potential density map. Particles extracted in 440x440 Fourier cropped to 360x360. This is a consensus/overall map. 50.0 emd_48625_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 -0.19035369 1.024966 0.0011008932 0.028258698 1.1538 1.1538 1.1538 AUTHOR Locally refined nucleosome from the Nucleosome Elongation Complex, resolved to 4.3 A emd_48625_additional_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 -0.19509014 0.89884585 0.0010640087 0.029366046 1.1538 1.1538 1.1538 AUTHOR Locally refined Pol II from the Nucleosome Elongation Complex, resolved to 4.3 A emd_48625_additional_3.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 Y X Z -0.13090104 0.5718973 0.001082451 0.024066893 1.1538 1.1538 1.1538 AUTHOR Composite map of the locally refined Pol II and nucleosome from the Nucleosome Elongation Complex. emd_48625_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 -0.32866934 1.0658395 0.0014649376 0.04423681 1.1538 1.1538 1.1538 AUTHOR Half map 1 from cryoSPARC emd_48625_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 -0.31201127 1.1466551 0.0014838534 0.044341788 1.1538 1.1538 1.1538 AUTHOR Half map 2 from cryoSPARC