Clustered regularly interspaced short palindromic repeats (CRISPRs) from Prevotella and Francisella 1 (Cpf1) are RNA-guided endonucleases that produce cohesive double-stranded breaks in DNA by specifically recognizing thymidine-rich protospacer-adjacent motif (PAM) sequences. Even though, Cpf1 is emerging as a powerful genome-editing tool and numerous structures of various Cpf1 proteins have been solved, the apo-structure of Cpf1 remains elusive. In this study, to understand native state of Cpf1 protein from Francisella novicida (FnCpf1), we determined two solution structure of FnCpf1 with and without CRISPR RNA (crRNA) using small-angle X-ray scattering. Also, we visualized apo-structure of FnCpf1 using negative staining electron microcopy. By comparing between the apo-structure of FnCpf1 and with crRNA-bound structure, we realized that their overall shapes were similar as a closed form, suggesting that conformational change upon crRNA binding to FnCpf1 is not drastic, but a local induced fit might occur to recognize PAM sequences. However, the apo Cpf1 from Moraxella bovoculi 237 (MbCpf1) was examined as an open form, indicating that MbCpf1 may have a large conformational change for crRNA binding changing from an open to a closed form. These results suggested that the crRNA-induced conformational changes in Cpf1 differ among species.