Extended Data Fig. 2. Cryo-EM reconstruction of the three conformations of the Core-UBE2T-ID-DNA complex from the ubiquitination reaction.

a, Flowchart of single particle cryo-EM data processing of the Core-UBE2T-ID-DNA complex in three different conformations. Consensus and focused maps are colored by local resolution and oriented as in Fig. 1b (slight rotations were applied for clarity). Focused reconstructions are shown in a combined view as labeled, with the corresponding masks shown in semi-transparent rendering in different colors. All reconstruction4/mask4 renderings are shown separately. The composite maps are also semi-transparent and are colored by subunit. The four graphs on the right show gold-standard FSC curves between two independently refined half-maps for the consensus and focused reconstructions, with the FSC cutoff 0.143 marked by horizontal dashed lines.

b, Left, density attributed to ubiquitin (yellow) extending from UBE2T in the 7.1 Å focused reconstruction (~20 % of the closed-ID Core-UBE2T-ID-DNA Ub+ particles), masked by mask4 of a. This density is absent in the low pass filtered reconstruction of the rest of the particles (right map, Ub−).

c, Cartoon representations of models rigid-body fitted into the Ub+ map: Core-UBE2T-ID-DNA in closed-ID conformation (colored as in Fig. 1d), ubiquitin (PDB 4BVU, yellow), and mono-ubiquitinated FANCD2 (gray, Ub orange) from ID^Ub (PDB 6VAE) superimposed on FANCD2. The ubiquitin C-terminus (“C” in black sphere) is closer to UBE2T Cys86 (labeled) than to FANCD2 Lys561 (labeled), which is at the opposite side of Cys86.

d, Superposition of UBE2T-Ub moieties (ubiquitin in yellow) and two other E2-Ub conjugates on UBE2T (ubiquitin from PDB 4AP4 in green, and that from 5TTE in blue, all E2 in magenta).

e, Gold-standard FSC plot between two independently refined half-maps for the Ub+ reconstruction, with the FSC cutoff 0.143 marked by horizontal dashed lines.