Fast 3D motif search of EM density maps using a locally normalized cross-correlation function.
Three-dimensional motif search is becoming increasingly important both in the search for molecular signatures within a tomographic reconstruction, at low resolution, and in the search for atomic structures within high-resolution cryo-EM maps of macromolecular complexes. The present work describes the implementation of a fast local correlation algorithm suitable for template matching in the SPIDER environment. Two examples are given, one in each of the areas of application: (i). within a 7.8A single-particle reconstruction of the Escherichia coli ribosome, four proteins and one RNA structure were located with high accuracy; (ii). within a cryo-tomogram of sarcoplasmic reticulum vesicles, ryanodine receptors were located in positions that agreed with expert knowledge.
Rath
B K
BK
Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.
Hegerl
R
R
Leith
A
A
Shaikh
T R
TR
Wagenknecht
T
T
Frank
J
J
D000465:Algorithms; D020816:Amino Acid Motifs; D020285:Cryoelectron Microscopy / Q000379:methods*; D004583:Electrons; D004926:Escherichia coli / Q000378:metabolism; D015233:Models, Statistical; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry; D019837:Ryanodine Receptor Calcium Release Channel / Q000737:chemistry; D012519:Sarcoplasmic Reticulum / Q000378:metabolism
D019837:Ryanodine Receptor Calcium Release Channel; D012313:RNA