Crystal structure of the Ire1KR32 oligomer obtained without ligands in the ATP pocket. (a) Ire1 kinase/RNase forms an oligomer with the synthetic ligand APY29 (crystal P21212) and with a 6-mer DNA oligonucleotide that served as a noncleavable mimic of Ire1's RNA substrate (crystal C222). The sequence dCdCdGdCdAdG of the oligonucleotide is derived from the splice site of HAC1 mRNA. The filaments in the P21212 and in the C222 structures pack using entirely different sets of crystal contacts. (b) Simulated annealing (2,000 K) NCS-averaged Fobs - Fcalc difference map of the twofold symmetric density in the RNase active site (contoured at 5.5 σ). (c) Simulated annealing (2,000 K) NCS-averaged Fobs - Fcalc omit map for the αC-helix (contoured at 5.5 σ) and for the activation loop (contoured at 4.5 σ) in the C222 structure (red). Omit maps were calculated with αC-helix and activation loop residues deleted from all seven monomers prior to refinement. Analogous maps calculated by simulated annealing without NCS restraints are shown in Additional file 1, Figure S7. (d) Superposition of CDK2 and Ire1KR32 in the apo-bound state (this work) and the ADP-bound state (PDB ID 2rio) shows that the αC-helix of apo-Ire1KR32 (in the C222 structure) occupies the same conformation as in Ire1 ADP and in CDK2 ADP cyclin complexes, which is distinct from that in the inactive apo-CDK2 structure.