Pre-Initiation Complex in 3D The regulation of gene expression is critical for almost every aspect of biology. Transcription—generating an RNA copy of a gene—requires the assembly of a large pre-initiation complex (PIC) at every RNA polymerase II (pol II) promoter. Roughly 32 proteins—the subunits of pol II and the general transcription factors—form a PIC that can recognize a minimal TATA-box promoter, select a transcription start site, and synthesize a nascent transcript. Murakami et al. (p. 10.1126/science.1238724 , published online 26 September; see the Perspective by Malik and Roeder ) determined the three-dimensional map of the Saccharomyces cerevisiae 30-subunit PIC using cryo-electron microscopy. The saddle-shaped TATA binding protein, the boot-shaped transcription factor IIA (TFIIA), and promoter DNA ∼27 bp downstream of the TATA-box could all be seen. Cross-linking and mass spectrometry was used to determine the spatial proximity of the 30 subunits, revealing that the PIC forms two lobes with TFIIF forming a bridge between them.