A comparison of the PB1 structure in the pre-initiation (grey) and elongation state (colors) as analyzed with DynDom (http://dyndom.cmp.uea.ac.uk/dyndom/). The thumb domain (~ 509–670) together with the PB2 N1 and N2 domains (PB2/54-153, ruby) rotate outwards by ~ 4.5° compared to the superposed palm domain (cyan). The movement is mediated by a hinge between the palm and thumb domains involving PB1 residues 508–509 and 533–538 (green). There is also a slight shift of the PA-C domain (not shown). We also quantified the consequence of this conformational change on the width of the active site cavity taken as the distance between the Cα atoms of PB1/Glu256 of helix α9 and PB1/Ile524 of helix α17. The width increases from ~ 30.7 Å in the pre-initiation state to ~ 31.4 Å in the initiation state and ~ 32.1 Å in the elongation state. The cavity is almost wide enough to fit A-form duplex RNA even in the pre-initiation state but must splay by ~ 1.4 Å to accommodate the extended product-template RNA duplex.