The E1 and E2 proteins of papillomaviruses are essential for the initiation of viral DNA replication. We have purified the E2 protein of human papillomavirus type 33 (HPV-33) by immunoaffinity chromatography. The purified E2 protein bound with high affinity to all four consensus binding sites of HPV-33 (Kd approximately equal to 2 x 10(-10)M). A putative E2 binding site differing at one position in the second stem of the palindrome was not bound by E2. The E1 protein of HPV-33 purified by affinity chromatography using glutathione S-transferase as tag displayed specific DNA-binding activity in footprint analyses protecting HPV-33 nucleotides 7896 to 7909/1 to 18 from DNasel digestion. Hypersensitive sites at position 6 on the sense and position 1 on the antisense strand were observed in the middle of the protected region. An E1/E2 complex protected the E1 binding site and E2 binding sites from DNasel digestion suggesting that both proteins retain DNA-binding activity in the complex.