Fig. 4

KArGO cross-linking of three protein complexes. a Number of KArGO-linked peptide pairs identified from each complex. b MS/MS spectrum of a pair of peptides cross-linked by KArGO from the CNGP complex. c Cross-links used for Rosetta docking of Nop10 to Cbf5, subunits of the CNGP complex. d Representative structure of Nop10 from the largest conformational cluster obtained after global docking with KArGO cross-links alone or with DSS plus ArGO1 cross-links, and superimposed on the native structure of the Nop10 subunit. e Amino-acid contact map depicting the K–R cross-links identified in ALPK1 NTD in the presence (blue) or absence (pink) of the ALPK1 kinase domain. Each circle represents a pair of KArGO-linked residues, marked with a number n or n’, which corresponds to the n^th cross-link in Supplementary Table 3. The prime symbol denotes a cross-link originating from NTD + KD. The radius of each circle correlates with the number of MS2 spectra identified for this cross-link (see Supplementary Table 3). f Concerning Utp15, Utp9, and Utp5, three subunits of a UtpA sub-complex, KArGO cross-links (cyan) provided more information about the interface between subunits than BS³ (red). The cross-links are mapped onto the cryo-EM structure⁶¹ and also shown in a xiNET⁶⁷ connectivity map. A single over-length cross-link (dashed line) is also shown in the connectivity map. g A connectivity map showing that all of the high-confidence BS³ (red) and KArGO (cyan) cross-links identified between Utp4 and Utp15 or Utp5 are over-length cross-links (dashed lines) when mapped onto the cryo-EM structure⁶¹