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Figure 7
The D2 domain of full-length p97 posed a challenge for `standard' refinement prior to the availability of a high-resolution structure of D2. We show a close-up view of the region around the nucleotide-binding site of D2 in complex with ADP. (a) The best available structure of p97 in this nucleotide state (gray; PDB entry 3cf3 ) is superimposed on the original structure (PDB entry 1yqi ), which was determined without knowledge of the D2 domain of the crystal structure (unavailable at the time). This original structure had severe problems, e.g. a wrong orientation of the ADP molecule and some register shifts in helices close to the nucleotide-binding site in the D2 domain (black arrows). (b) The original structure (PDB entry 1yqi ) was re-refined with DEN as described in the text. It yielded a considerably improved structure (red), with corrected register shifts and position of the nucleotide. (c) `Standard' refinement (orange; see text) did not move the model closer to the true structure and could not correct the position of the nucleotide. Loops and α-helices show significant differences from the DEN-refined structure (red).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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