Previous X-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A previous structure at 4.5 Å resolution of an RNA polymerase II–general transcription factor TFIIB complex revealed the N-terminal region of TFIIB, including a loop termed the “B-finger” reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the C-terminal region. A new crystal structure of the same complex at 3.8 Å resolution obtained under different solution conditions is complementary with the previous one, revealing the C-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B-finger. In the new structure, the linker between the N- and C-terminal regions can also be seen, snaking down from above the cleft towards the active center. The two structures, taken together with others previously obtained, dispel longstanding mysteries of the transcription initiation process.