Fig. 5: Cross-linking of the TATA-box binding transcription factor TBP.

a Overview of the four identified cross-links on three unique peptides. Blue background indicates information obtained from cross-linking experiments and gray background information obtained from the crystal structure (PDB ID: 1C9B⁴¹). Red letters indicate possible cross-linked amino acids or cross-linked nucleotides, respectively. b Schematic view of the domain structure of TBP, the TATA box (gray shading), and surrounding nucleotides, as well as the cross-links. c Crystal structure of TBP bound to an extended Adml promoter (PDB ID: 1C9B⁴¹). Location of the cross-link of N257 to one of the two thymidines (green) and of the cross-links of amino acid V220 to deoxyadenosine (orange) and A211 to deoxycytidine (light green). Cross-linked amino acids are depicted in red, the peptide ²⁵⁵IQNMVGSCDVK²⁶⁵ in light red, and the peptide ²⁰⁹TTALIFSSGKMVCTGAK²²⁵ in blue. Dashed lines represent the distance of amino acid to nucleotide and distance is shown above the line. d MS2 ion series and spectra of the cross-linked TTALIFSSGKMVCTGAK peptide. Abbreviations in the MS2 spectra and MS2 ion series: caret: neutral loss of CH₄SO, Tox: trioxidated cysteine (cysteic acid). Other abbreviations as in Fig. 4.