Author affiliation (other than CSIC): Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK.The recognition of specific signals encoded within the 3′-untranslated region of the newly transcribed mRNA triggers the assembly of a multiprotein machine that modifies its 3′-end. Hrp1 recognises one of such signals, the so-called polyadenylation enhancement element (PEE), promoting the recruitment of other polyadenylation factors in yeast. The molecular bases of this interaction are revealed here by the solution structure of a complex between Hrp1 and an oligonucleotide mimicking the PEE. Six consecutive bases (AUAUAU) are specifically recognised by two RNA-binding domains arranged in tandem. Both protein and RNA undergo significant conformational changes upon complex formation with a concomitant large surface burial of RNA bases. Key aspects of RNA specificity can be explained by the presence of intermolecular aromatic–aromatic contacts and hydrogen bonds. Altogether, the Hrp1–PEE structure represents one of the first steps towards understanding of the assembly of the cleavage and polyadenylation machinery at the atomic level.This work has been financed by a individual Marie Curie Fellowship of the European Community Human Potential Program (HPRMF-CT-2000-00722).Peer reviewed