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Figure 2
Illustrative examples of successful coiled-coil structure solution with AMPLE. In each case, the target chain of the crystal structure is shown on the left as a green cartoon, MR-placed model(s) as blue lines and (where appropriate) cartoons, and the ensemble search model is displayed on the right in blue. MR-placed model ensembles (a–d, g–h) are represented here, for clarity, by their first member. (a) In-register placement (i.e. the sequence of the search model correctly aligns with that of the substrate) of two copies of a mildly truncated centroid structure as a search model solves the coiled-coil domain structure of the Sin nombre virus nucleocapsid protein (PDB entry 2ic9 ). (b) Out-of-register placement (the backbone structures of the search model and target coincide closely, but their sequences do not match) of eight copies of a heavily truncated search-model ensemble with polyalanine side-chain treatment solves a coiled-coil fragment from the HIV-1 protein gp41 (PDB entry 3h00 ). (c) Four copies of an ensemble with reliable side-chain treatment solves the coiled-coil domain structure from the replication regulator geminin (PDB entry 1uii ). (d) A heavily truncated polyalanine search model solves the structure of adhesin UspA1 (PDB entry 2qih ). (e) Two copies of a five-residue ideal polyalanine helix solved a de novo-designed assembly protein (PDB entry 3s0r ; 2.45 Å). (f) Two copies of a 20-residue ideal polyalanine helix solved a dynamin adaptor protein (PDB entry 2xu6 ; 2.7 Å). (g) Five copies of a mildly truncated polyalanine search model ensemble solved the complex of the GGA1 GAT domain (yellow) with the GAT-binding domain of rabaptin 5 (green) (PDB entry 1x79 ; 2.4 Å). (h) Four copies of a polyalanine search model ensemble solved a transcription-regulation complex (PDB entry 1h8a ; 2.23 Å) containing a coiled-coil domain (green), an additional helical protein (yellow) and duplex DNA (brown).

IUCrJ
Volume 2| Part 2| February 2015| Pages 198-206
ISSN: 2052-2525
doi:10.1107/S2052252515002080