We report the crystal structure of N-utilizing substance A protein (NusA) from Thermotoga maritima (TmNusA), a protein involved in transcriptional pausing, termination, and antitermination. TmNusA has an elongated rod-shaped structure consisting of an N-terminal domain (NTD, residues 1-132) and three RNA binding domains (RBD). The NTD consists of two subdomains, the globular head and the helical body domains, that comprise a unique three-dimensional structure that may be important for interacting with RNA polymerase. The globular head domain possesses a high content of negatively charged residues that may interact with the positively charged flaplike domain of RNA polymerase. The helical body domain is composed of a three-helix bundle that forms a hydrophobic core with the aid of two neighboring β-strands. This domain shows structural similarity with one of the helical domains of σ 70 factor from Escherichia coli. One side of the molecular surface shows positive electrostatic potential suitable for nonspecific RNA interaction. The RBD is composed of one S1 domain and two K-homology (KH) domains forming an elongated RNA binding surface. Structural comparison between TmNusA and Mycobacterium tuberculosis NusA reveals a possible hinge motion between NTD and RBD. In addition, a functional implication of the NTD in its interaction with RNA polymerase is discussed.