Crystal structures of the NEMO CC2-LZ domain. (A) Helical wheel representation of the NEMO CC2-LZ structure, starting from residue A288 at position a and ending at residue R319 at position a. The residues A288 and D311 are shown in red and purple, respectively. (B) Cartoon representation of the entire NEMO CC2-LZ structure showing domain organization (residues 258-344). Residues A288 and D311, which are located in the CC2 and NOA-LZ domains, respectively, are shown as ball and stick representations. CC2 indicates coiled coil 2; NOA, ubiquitin-binding site; and LZ, leucine zipper. (C) Structural comparison of the CC2-LZ domain in complex with a K63-linked diubiquitin chain (Di-Ub; green) or a linear diubiquitin chain (magenta). Ub indicates ubiquitin. The superimposition was achieved by Ca alignment of residues 300-322 (RMSD: 0.603 Å). NEMO helices in the complex with linear diubiquitin are shown in blue, whereas those in complex with K63-linked diubiquitin are shown in red. (Bottom) Zoom view of the NOA ubiquitin-binding site showing the interaction between the D311 residue and the R72 residue located in the distal ubiquitin C-terminal tail. In both complexes, the D311 side chain of NEMO forms a specific intermolecular salt bridge with the R72 side chain of the K63-linked (green) or linear (magenta) diubiquitin linker.