Table 2 Nucleotide occupancy of subunits in ClpXP structures

Structure	Subunit position in ClpX spiral						Seam subunit confirmation	ClpX state	ATPγS	Walker-B mutation
	1	2	3	4	5	seam
8V9R	Ta	Tb	Tc	Dd	De	Df	Up	Substrate-engaged	No	No
9C87	Ta	Tb	Tc	Dd	De	Df	Up	Substrate-engaged	No	No
9C88	Ta	Tb	Tc	Dd	De	Df	Up	Translocation	No	No
6PP7/6POD	Tb	Tc	Td	Te	tf	Da	Up	Translocation	Yes	Yes
6WSG	Tb	Tc	Td	Te	tf	Da	Up	Translocation pre-engagment	Yes	No
6VFS	Tb	Tc	Td	Te	Df	Da	Up	Translocation	No	Yes
8ET3	Ta	Tb	Tc	Td	De	Df	Up	Adaptor substrate recognition	Yes	No
6PP8/6POS	Ta	Tb	Tc	Td	Te	Df	Down	Substrate-bound*	Yes	Yes
6PP6/6PO3	Ta	Tb	Tc	Td	Te	Df	Down	Substrate-bound*	Yes	Yes
6PP5/6PO1	Ta	Tb	Tc	Td	Te	Df	Down	Translocation	Yes	Yes
6WRF	Ta	Tb	Tc	Td	Te	Df	Down	ssrA-tag recognition	Yes	No
6VFX	Ta	Tb	Tc	Td	Te	Df	Down	Translocation	No	Yes
8E91	Ta	Tb	Tc	Td	De	Df	Down	Substrate-free	Yes	No
8E8Q	Ta	Tb	Tc	Td	De	Df	Down	Substrate-free	No	No
8E7V	Ta	Tb	Tc	Td	De	Df	Down	Substrate-free	No	No

‘T’ denotes a nucleoside triphosphate (ATP or ATPγS) in which the ‘Arg-finger’ side chain of residue 307 from an adjacent subunit appears to be in a conformation that would support hydrolysis. ‘t’ denotes a nucleoside triphosphate in a site in which Arg³⁰⁷ is disengaged. ‘D’ represents ADP. Subscripts following the nucleotide designation are the chain identity of the subunit in the PDB file. In structures with PDB codes 6PP8/6POS and 6PP6/6PO3, native structure of an unknown substrate/adaptor or ensemble of substrates was present above the ClpX channel, but the resolution was too poor to determine if there was a direct connection to polypeptide density in the axial channel. In this instance, the ClpX state is noted as substrate-bound*. The remaining ClpX states were defined as follows. In the ssrA-tag recognition state, the axial channel of ClpX is closed and is interacting with the C-terminus of the degron tag, which is above this point of closure. In contrast, structures of the substrate-engaged and translocation states all exhibit an open axial channel of ClpX, with either the degron tag or the unfolded substrate threaded through the opening. In the substrate-engaged-state (reported here), the folded domain of the substrate is resolved and observed to make contact with the axial channel. In translocation state, the substrate is unresolved and sidechains of the substrate polypeptide in the axial channel cannot be assigned.

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