A number of beta-microseminoproteins (MSPs) have been identified from different species. MSPs are all non-glycosylated and disulfide bond-rich, but show a relatively low level of conservation. Although all Cys residues are conserved, our previous study showed that the disulfide bond pairings differ in porcine and ostrich MSPs. Despite the variety of biological functions that have been suggested for MSPs, their real function is still poorly understood. Furthermore, no 3D structure has been reported for any MSP, so the determination of the structure and function of MSPs is an interesting and important task. In the present study, we determined the 3D solution structure of porcine MSP on the basis of 1018 restraints. The ensemble of 20 NMR structures was well defined, with average root-mean-square deviations of 0.83(+/-0.16) A for the backbone atoms and 1.37(+/-0.17) A for heavy-atoms in residues 2-90. The 3D structure showed that porcine MSP is clearly composed of two domains, an N-terminal domain consisting of one double-stranded and one four-stranded antiparallel beta-sheet, and a C-terminal domain consisting of two double-stranded antiparallel beta-sheet. The orientation of the two domains was derived mainly on the basis of long-range NOEs and verified using residual dipolar coupling data. No inter-domain hydrophobic interaction or H-bonding was detected. However, a number of charged residues were found in close proximity between the domains, indicating that electrostatic interaction may be the key factor for the orientation of the two domains. This is the first report of a 3D structure for any MSP. In addition, structural comparison based on distance matrix alignment (DALI), class architecture topology and homologous superfamily (CATH) and combinatorial extension (CE) methods revealed that porcine MSP has a novel structure with a new fold providing valuable information for future structural studies on other MSPs and for understanding their biological functions.