Non-proline cis peptide bond is rarely found in proteins. The recent surveys revealed that this unusual peptide configuration is by no means a curiosity, but overwhelmingly occurs at functionally important sites. However one still doubts whether it is related to crystal packing interactions, since all non-proline cis peptide bonds identified so far are from crystal structures. A toxin BmK M1 from the scorpion Buthus martensii Karsch have been crystallized as a dimer in space group P212121 with unit-cell dimensions a = 76.39 (A),b=52.77 (A), c=27.12 (A). This dimeric structure was solved by molecular replacement and refined to R=0.109 for all reflections at a resolution of 1.4 (A). The extensively refined structure definitely shows that the cis peptide bond Pro9-His10 equally occurs in both molecule A and molecule B in the dimer. The observation manifested that this striking non-proline cis peptide is not related to crystal packing, but caused by certain intrinsic factors. The detailed analyses and comparison with the structure of BmK M8, which is homologous to M1 but has trans peptide bond 9-10, showed that the five-residue reverse (8 ～12) with a consensus sequence (-KPXNC-) may be the intrinsic structural element for the cis form of this peptide bond. A pair of well organized main-chain hydrogen bond between residues 10 in cis unit and 64 at C-terminus forms main tertiary interactions to stabilize this energetically unfavorable peptide bond.