After purification of EC* by size exclusion chromatography and mild crosslinking with 85 glutaraldehyde, we determined its cryo-EM structure at a nominal resolution of 3.1 Å (Fig. 2, 86 Supplementary Video 1, Extended Data Fig. 2j). 2D classification revealed densities on the 87 Pol II surface (Extended Data Fig. 3, 4; Extended Data Table 2) and resulted in a 3D 88 reconstruction from 374,964 particles. The core of Pol II extended to ~2.6 Å resolution. 89 Vos et al.,: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6Elongation factors were resolved at lower resolutions (~12 Å for the most flexible domains), 90 and their corresponding densities were improved by focused classification and refinement 91 (Extended Data Figs. 3-5, Methods). This led to a total of eight cryo-EM density maps that 92 enabled us to fit available structures and homology models (Extended Data Fig. 3; 93 Supplementary Table 1). Modeling was aided by lysine crosslinking data (Extended Data 94 Fig. 6, Supplementary Tables 2-4). 225 unique crosslinks were detected in structured regions, 95 of which 210 fell into the permitted 30 Å range. The remaining 15 crosslinks formed between 96 mobile elements of the structure (Extended Data Fig. 6; Supplementary Table 2). 97 To complete the EC* structure, we determined the crystal structure of the isolated 98 human SPT6 tandem SH2 (tSH2) domain at 1.8 Å resolution, and unambiguously docked this 99 new structure into the corresponding density of EC* (Fig. 3, Methods, Extended Data Fig. 5f, 100 6f, 7, Extended Data Table 3). The resulting structure of EC* shows good stereochemistry 101 and lacks only mobile regions, including the terminal regions of PAF1 and LEO1, most of 102 CDC73, the acidic N-terminal region of SPT6, and the C-terminal extensions of SPT5, SPT6, 103 and CTR9 ( Supplementary Table 1). 104 105 PAF and SPT6 structure and contacts 106 DSIF, PAF, and SPT6 are modular proteins that coat the outer surface of Pol II (Fig. 2). DSIF 107 domains are arrayed around the Pol II cleft and RNA exit tunnel 4 . PAF extends along the RPB2 108 side and docks on the Pol II funnel. PAF is anchored to the external domains of RPB2 via its 109 PAF1-LEO1 dimerization module (Fig. 2b, c). The central PAF subunit CTR9 contains 19 110 tetratricopeptide repeats (TPRs; residues 41-750) that each form two antiparallel ɑ-helices ( Fig. 111 3a, Supplementary Table 6, Extended Data Fig. 5b). The CTR9 TPRs form a right-handed 112 superhelix that extends from the Pol II subunit RPB11 along RPB8 via the polymerase funnel 113 to the foot (Fig. 3a). The TPRs are followed by a pair of helices that create a 'vertex' and 114 connect to a prominent 'trestle' helix in CTR9 (CTR9 residues 807-892) (Extended Data Fig. 115 5c). The trestle extends ~100 Å from the Pol II foot to subunit RPB5 where downstream DNA 116 enters the Pol II cleft. The vertex and TPRs 13, 14, and 18 buttress the PAF subunit WDR61, 117 which forms a seven-bladed β-propeller 28 and faces away from Pol II (Fig. 3a, Extended Data 118 Fi...

How Integrator ends transcription early Transcription is the central process that activates the genetic information in cells, but our understanding of how gene transcription is regulated is incomplete. The so-called Integrator can stop the transcribing enzyme RNA polymerase II at the beginning of genes, but how such downregulation of transcription occurs is unclear. Fianu et al . present the three-dimensional structure of Integrator bound to the transcribing polymerase complex, providing molecular and mechanistic insights into how Integrator mediates transcription regulation. —DJ