Extended Data Fig. 2: Cross-linking mass-spectrometry interaction networks. | Nature

Extended Data Fig. 2: Cross-linking mass-spectrometry interaction networks.

From: Structural basis of human transcription–DNA repair coupling

Extended Data Fig. 2

a, Cross-linking mass-spectrometry interaction network within the Pol II-CSA-DDB1-CSB-UVSSA complex after crosslinking with BS3. (right) Crosslinks with the score above 3 that were detected at least twice are shown. (left) Crosslinks were mapped onto the Pol II-CSA-DDB1-CSB structure. Coloured rods connecting crosslinked residues represent permitted (blue) or non-permitted (red) crosslinking distances. 89% of mapped crosslink sites fall within the permitted crosslinking distance of 30 Å. 11% of crosslinks in violation of crosslinking distance are likely a result of complex flexibility or technical errors. Histogram shows the number of crosslinks detected at a particular crosslinking distance. b, Cross-linking mass-spectrometry interaction network within the Pol II-CSA-DDB1-CSB-UVSSA complex after crosslinking with EDC. (left) Crosslinks with the score above 3 that were detected at least twice are shown. (right) Crosslinks were mapped onto the Pol II-CSA-DDB1-CSB structure. 83% of mapped crosslink sites fall within the permitted crosslinking distance of 20 Å. 17% of crosslinks in violation of crosslinking distance are likely a result of complex flexibility or technical errors. Histogram shows the number of crosslinks detected at a particular crosslinking distance. c, BS3 crosslinks with a score above 3 that were detected at least twice and mapped onto Pol II. The Pol II surface area within the 30 Å radius of the crosslink site was colored as a protein footprint. d, BS3 and EDC crosslinks used to identify the CSA-interacting motif (CIM) in CSB.

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